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
8058,ERR022485,ERX008920,ERS017423,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 6hpf,SAMEA898399,Wellcome Sanger Institute,Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 6hpf,RNA from Zebrafish embryo 6hpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_6.srf,srf,5910514528.0,38884964.0,E MTAB 434:4946 6.srf,0:76 1:76,A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807,76,76,,,1741038828,1243493514,1214904056,1703863323,7214807,ERX008920,ERS017423,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.91619,0.91684,0.14961,0.15221,0.77189,0.7723,0.49092,0.49303,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Gastrula,Embryo,Whole Organism,All anatomical structures
40711,SRR3420419,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz,fastq fastq,2419781176.0,15919613.0,AG00719 run 1,0:76 1:76,A:738997601;C:465047900;G:477140497;T:733241052;N:5354126,76,76,,,738997601,465047900,477140497,733241052,5354126,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.78184,0.71182,0.66469,0.60037,0.75743,0.77518,0.53432,0.52801,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40712,SRR3420420,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz,fastq fastq,3074724552.0,20228451.0,AG00719 run 2,0:76 1:76,A:918671897;C:609510609;G:622542852;T:922439528;N:1559666,76,76,,,918671897,609510609,622542852,922439528,1559666,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76444,0.65488,0.65157,0.55185,0.75741,0.78106,0.53067,0.52622,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40713,SRR3420421,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz,fastq fastq,2666395856.0,17542078.0,AG00719 run 3,0:76 1:76,A:787508876;C:539791618;G:549145516;T:785088342;N:4861504,76,76,,,787508876,539791618,549145516,785088342,4861504,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.75479,0.69465,0.63843,0.58422,0.75716,0.78423,0.53952,0.52615,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40714,SRR3420388,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz,fastq fastq,2699903800.0,17762525.0,AG00718 run 1,0:76 1:76,A:832300161;C:503956886;G:525141498;T:832566681;N:5938574,76,76,,,832300161,503956886,525141498,832566681,5938574,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76651,0.69033,0.63937,0.56749,0.77145,0.78545,0.53429,0.53165,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40715,SRR3420392,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz,fastq fastq,2798947456.0,18414128.0,AG00718 run 2,0:76 1:76,A:853546590;C:536347349;G:556751964;T:851863324;N:438229,76,76,,,853546590,536347349,556751964,851863324,438229,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74665,0.63683,0.6265,0.5237,0.76134,0.7905,0.54613,0.53982,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40716,SRR3420398,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz,fastq fastq,1442918520.0,9492885.0,AG00717 run 1,0:76 1:76,A:442675510;C:273265985;G:284514997;T:439403136;N:3058892,76,76,,,442675510,273265985,284514997,439403136,3058892,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76736,0.69048,0.60693,0.53532,0.74647,0.76138,0.51546,0.5135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40717,SRR3420402,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz,fastq fastq,2524099688.0,16605919.0,AG00717 run 2,0:76 1:76,A:752163917;C:500880325;G:526291920;T:744462824;N:300702,76,76,,,752163917,500880325,526291920,744462824,300702,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.7274,0.651,0.57791,0.50498,0.74434,0.76329,0.51831,0.50479,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40718,SRR3420405,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz,fastq fastq,1320586032.0,8688066.0,AG00717 run 3,0:76 1:76,A:394339370;C:259687848;G:270914284;T:389960707;N:5683823,76,76,,,394339370,259687848,270914284,389960707,5683823,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72219,0.6734,0.55665,0.5122,0.75371,0.76323,0.5098,0.50658,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40719,SRR3420409,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz,fastq fastq,1778143272.0,11698311.0,AG00717 run 4,0:76 1:76,A:531893644;C:351009327;G:366187476;T:528937189;N:115636,76,76,,,531893644,351009327,366187476,528937189,115636,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72027,0.6573,0.57252,0.50814,0.74913,0.77479,0.51537,0.50066,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40720,SRR3420315,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz,fastq fastq,1837024424.0,12085687.0,AG00716 run 1,0:76 1:76,A:571581150;C:339887376;G:357200726;T:564453542;N:3901630,76,76,,,571581150,339887376,357200726,564453542,3901630,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.77818,0.69777,0.64211,0.56481,0.75503,0.76926,0.50584,0.51507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40721,SRR3420319,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz,fastq fastq,2763994600.0,18184175.0,AG00716 run 2,0:76 1:76,A:841712204;C:530711238;G:562110067;T:828853061;N:608030,76,76,,,841712204,530711238,562110067,828853061,608030,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74716,0.66787,0.61425,0.53764,0.7475,0.76518,0.50855,0.51311,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40722,SRR3420323,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz,fastq fastq,1055704904.0,6945427.0,AG00716 run 3,0:76 1:76,A:323142351;C:199674907;G:210508599;T:317806564;N:4572483,76,76,,,323142351,199674907,210508599,317806564,4572483,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.73664,0.68701,0.59387,0.5447,0.76179,0.76132,0.51299,0.51552,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40723,SRR3420327,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz,fastq fastq,2526928408.0,16624529.0,AG00716 run 4,0:76 1:76,A:771333886;C:482964782;G:508687112;T:763609426;N:333202,76,76,,,771333886,482964782,508687112,763609426,333202,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74535,0.66478,0.61452,0.53584,0.75826,0.77329,0.51139,0.51539,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
41382,SRR4375306,SRX2226799,SRS1732692,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B3,resa AG01070,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B3,AG01070.1,AG01070.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz,fastq fastq,601712368.0,3958634.0,AG01070.1 R2.fastq.gz,0:76 1:76,A:188474921;C:113643606;G:114382568;T:185195364;N:15909,76,76,,,188474921,113643606,114382568,185195364,15909,SRX2226799,SRS1732692,SRA482696,Yale University|Genetics,Yale University,2,0.84037,0.84016,0.03493,0.03544,0.97303,0.97252,0.46337,0.47093,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41383,SRR4375305,SRX2226798,SRS1732691,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B2,resa AG01069,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B2,AG01069.1,AG01069.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz,fastq fastq,1344477848.0,8845249.0,AG01069.1 R1.fastq.gz,0:76 1:76,A:418545593;C:256422789;G:257715519;T:411760293;N:33654,76,76,,,418545593,256422789,257715519,411760293,33654,SRX2226798,SRS1732691,SRA482696,Yale University|Genetics,Yale University,2,0.84542,0.84566,0.03642,0.03588,0.97084,0.97197,0.4739,0.48121,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41384,SRR4375304,SRX2226797,SRS1732690,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B1,resa AG01068,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B1,AG01068.1,AG01068.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz,fastq fastq,896200056.0,5896053.0,AG01068.1 R2.fastq.gz,0:76 1:76,A:278768309;C:171161843;G:172303088;T:273944252;N:22564,76,76,,,278768309,171161843,172303088,273944252,22564,SRX2226797,SRS1732690,SRA482696,Yale University|Genetics,Yale University,2,0.83862,0.83897,0.0351,0.03585,0.97183,0.97204,0.47364,0.47138,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41385,SRR4375303,SRX2226796,SRS1732689,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B3,resa AG01067,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B3,AG01067.1,AG01067.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz,fastq fastq,1799778192.0,11840646.0,AG01067.1 R1.fastq.gz,0:76 1:76,A:561491448;C:342221462;G:343998479;T:552022535;N:44268,76,76,,,561491448,342221462,343998479,552022535,44268,SRX2226796,SRS1732689,SRA482696,Yale University|Genetics,Yale University,2,0.84432,0.84397,0.03554,0.03522,0.97224,0.9725,0.46732,0.46922,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41386,SRR4375302,SRX2226795,SRS1732688,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B2,resa AG01066,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B2,AG01066.1,AG01066.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz,fastq fastq,1313436864.0,8641032.0,AG01066.1 R2.fastq.gz,0:76 1:76,A:409666264;C:249755645;G:251028600;T:402953610;N:32745,76,76,,,409666264,249755645,251028600,402953610,32745,SRX2226795,SRS1732688,SRA482696,Yale University|Genetics,Yale University,2,0.84584,0.84611,0.0349,0.03543,0.97189,0.97175,0.47547,0.48555,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41387,SRR4375301,SRX2226794,SRS1732687,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B1,resa AG01065,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B1,AG01065.1,AG01065.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz,fastq fastq,1442385152.0,9489376.0,AG01065.1 R2.fastq.gz,0:76 1:76,A:449362282;C:274879749;G:276626223;T:441480173;N:36725,76,76,,,449362282,274879749,276626223,441480173,36725,SRX2226794,SRS1732687,SRA482696,Yale University|Genetics,Yale University,2,0.8417,0.84205,0.03519,0.03559,0.97193,0.97179,0.47697,0.46118,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41390,SRR4375197,SRX2226727,SRS1732683,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B3,resa AG01086,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B3,AG01086.2,AG01086.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz,fastq fastq,714848400.0,4702950.0,AG01086.2 R2.fastq.gz,0:76 1:76,A:261928616;C:96586565;G:97768464;T:258351392;N:213363,76,76,,,261928616,96586565,97768464,258351392,213363,SRX2226727,SRS1732683,SRA482696,Yale University|Genetics,Yale University,2,0.00715,0.00733,0.00046,0.00044,0.99417,0.99435,0.46775,0.42207,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41392,SRR4375175,SRX2226709,SRS1732683,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B3,resa AG01086,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B3,AG01086.1,AG01086.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz,fastq fastq,411922128.0,2710014.0,AG01086.1 R1.fastq.gz,0:76 1:76,A:150812258;C:55795177;G:56809368;T:148495332;N:9993,76,76,,,150812258,55795177,56809368,148495332,9993,SRX2226709,SRS1732683,SRA482696,Yale University|Genetics,Yale University,2,0.00798,0.00746,0.00062,0.00055,0.99385,0.99399,0.44328,0.47308,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41393,SRR4375146,SRX2226694,SRS1732682,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B2,resa AG01085,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B2,AG01085.2,AG01085.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz,fastq fastq,700337720.0,4607485.0,AG01085.2 R1.fastq.gz,0:76 1:76,A:256568404;C:94627005;G:95783677;T:253149693;N:208941,76,76,,,256568404,94627005,95783677,253149693,208941,SRX2226694,SRS1732682,SRA482696,Yale University|Genetics,Yale University,2,0.00733,0.00726,0.00055,0.00048,0.99413,0.99393,0.46893,0.45795,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41394,SRR4375102,SRX2226674,SRS1732682,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B2,resa AG01085,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B2,AG01085.1,AG01085.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz,fastq fastq,409587712.0,2694656.0,AG01085.1 R1.fastq.gz,0:76 1:76,A:149931448;C:55481183;G:56493706;T:147671446;N:9929,76,76,,,149931448,55481183,56493706,147671446,9929,SRX2226674,SRS1732682,SRA482696,Yale University|Genetics,Yale University,2,0.0079,0.0078,0.00056,0.0005,0.99366,0.99385,0.42647,0.47214,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41395,SRR4375101,SRX2226673,SRS1732681,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B1,resa AG01084,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B1,AG01084.2,AG01084.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz,fastq fastq,396825488.0,2610694.0,AG01084.2 R1.fastq.gz,0:76 1:76,A:145317384;C:53679748;G:54375412;T:143331621;N:121323,76,76,,,145317384,53679748,54375412,143331621,121323,SRX2226673,SRS1732681,SRA482696,Yale University|Genetics,Yale University,2,0.0071,0.00673,0.00044,0.00042,0.99417,0.99419,0.44659,0.45357,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41396,SRR4375100,SRX2226672,SRS1732681,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B1,resa AG01084,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B1,AG01084.1,AG01084.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz,fastq fastq,236514888.0,1556019.0,AG01084.1 R1.fastq.gz,0:76 1:76,A:86560104;C:32062698;G:32664624;T:85221432;N:6030,76,76,,,86560104,32062698,32664624,85221432,6030,SRX2226672,SRS1732681,SRA482696,Yale University|Genetics,Yale University,2,0.00756,0.00706,0.00061,0.00064,0.99405,0.99419,0.47228,0.48736,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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
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
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
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
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
43144,SRR5893111,SRX3058734,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,AG01047.2,AG01047.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.2_R1.fastq.gz,fastq,42440299.0,1862352.0,AG01047.2 R1.fastq.gz,0:22.79 1:0,A:11644782;C:9368619;G:10136237;T:11289519;N:1142,22,0,,,11644782,9368619,10136237,11289519,1142,SRX3058734,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.55293,,0.13885,,0.79379,,0.59223,,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
43149,SRR5893116,SRX3058729,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,AG01047.6,AG01047.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.6_R1.fastq.gz,fastq,450514845.0,19728387.0,AG01047.6 R1.fastq.gz,0:22.84 1:0,A:124287698;C:99171890;G:106632738;T:120420206;N:2313,22,0,,,124287698,99171890,106632738,120420206,2313,SRX3058729,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.57005,,0.14316,,0.78806,,0.59387,,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
43150,SRR5893117,SRX3058728,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,AG01047.5,AG01047.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.5_R1.fastq.gz,fastq,1004009476.0,43664444.0,AG01047.5 R1.fastq.gz,0:22.99 1:0,A:276219561;C:220490343;G:237521478;T:269709007;N:69087,22,0,,,276219561,220490343,237521478,269709007,69087,SRX3058728,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.57878,,0.14525,,0.78841,,0.58513,,28,,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
43155,SRR8782107,SRX3058723,SRS2404547,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B5,miniresa AG01735,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:5|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h pA RNA B5,AG01735.1,AG01735.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893122_replace_R1.fastq.gz,fastq,172767228.0,2273253.0,SRR5893122 replace R1.fastq.gz,0:76,A:46635317;C:32625014;G:34801109;T:58688753;N:17035,76,,,,46635317,32625014,34801109,58688753,17035,SRX3058723,SRS2404547,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94143,,2e-05,,0.99768,,0.61729,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
43156,SRR8782106,SRX3058722,SRS2404548,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B4,miniresa AG01734,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h pA RNA B4,AG01734.1,AG01734.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893123_replace_R1.fastq.gz,fastq,162402500.0,2136875.0,SRR5893123 replace R1.fastq.gz,0:76,A:43702648;C:30815303;G:32732910;T:55135738;N:15901,76,,,,43702648,30815303,32732910,55135738,15901,SRX3058722,SRS2404548,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94147,,0.0,,0.99791,,0.62083,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
43157,SRR8782105,SRX3058721,SRS2404549,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B4,miniresa AG01740,,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:4|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h a Am pA RNA B4,AG01740.1,AG01740.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893124_replace_R1.fastq.gz,fastq,155277424.0,2043124.0,SRR5893124 replace R1.fastq.gz,0:76,A:41889716;C:29676013;G:31219225;T:52477242;N:15228,76,,,,41889716,29676013,31219225,52477242,15228,SRX3058721,SRS2404549,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94462,,1e-05,,0.99772,,0.61448,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
43158,SRR8782103,SRX3058720,SRS2404550,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B3,miniresa AG01739,,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:3|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h a Am pA RNA B3,AG01739.1,AG01739.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893125_replace_R1.fastq.gz,fastq,141372692.0,1860167.0,SRR5893125 replace R1.fastq.gz,0:76,A:38036177;C:26891347;G:28463167;T:47966401;N:15600,76,,,,38036177,26891347,28463167,47966401,15600,SRX3058720,SRS2404550,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94098,,2e-05,,0.99772,,0.59143,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
43161,SRR8782102,SRX3058717,SRS2404552,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B3,miniresa AG01733,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h pA RNA B3,AG01733.1,AG01733.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893128_replace_R1.fastq.gz,fastq,157427692.0,2071417.0,SRR5893128 replace R1.fastq.gz,0:76,A:42152442;C:29932220;G:31835355;T:53490989;N:16686,76,,,,42152442,29932220,31835355,53490989,16686,SRX3058717,SRS2404552,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.93866,,0.0,,0.99772,,0.61232,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
43163,SRR8782099,SRX3058715,SRS2404555,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 B5,miniresa AG01741,,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:5|BioSampleModel:Model organism or animal,,,,,,,,,miniRESA   6h a Am pA RNA B5,AG01741.1,AG01741.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,SRR5893130_replace_R1.fastq.gz,fastq,164648756.0,2166431.0,SRR5893130 replace R1.fastq.gz,0:76,A:45004769;C:30908007;G:32493517;T:56226269;N:16194,76,,,,45004769,30908007,32493517,56226269,16194,SRX3058715,SRS2404555,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.93749,,3e-05,,0.99782,,0.62705,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-03-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48362,SRR5893048,SRX3058797,SRS2404520,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield pA B1,dev timecourse AG00658,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:3|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield pA B1,AG00658.1,AG00658.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00658.1_R2.fastq.gz AG00658.1_R1.fastq.gz,fastq fastq,2368759640.0,15583945.0,AG00658.1 R2.fastq.gz,0:76 1:76,A:643327175;C:540895938;G:540699719;T:641357257;N:2479551,76,76,,,643327175,540895938,540699719,641357257,2479551,SRX3058797,SRS2404520,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.89596,0.89407,0.07479,0.07678,0.76004,0.7595,0.48733,0.48807,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48363,SRR5893049,SRX3058796,SRS2404521,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield pA B2,dev timecourse AG00659,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:3|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield pA B2,AG00659.1,AG00659.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00659.1_R1.fastq.gz AG00659.1_R2.fastq.gz,fastq fastq,2038811568.0,13413234.0,AG00659.1 R2.fastq.gz,0:76 1:76,A:558819941;C:458698081;G:460805877;T:558399462;N:2088207,76,76,,,558819941,458698081,460805877,558399462,2088207,SRX3058796,SRS2404521,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.92967,0.92885,0.0788,0.08121,0.75661,0.75631,0.49269,0.49182,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2017-08-03,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48367,SRR5893065,SRX3058780,SRS2404535,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am shield pA B2,dev timecourse AG00701,,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:9|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am shield pA B2,AG00701.1,AG00701.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00701.1_R1.fastq.gz AG00701.1_R2.fastq.gz,fastq fastq,2611389944.0,17180197.0,AG00701.1 R1.fastq.gz,0:76 1:76,A:696886025;C:607737206;G:605609129;T:699045963;N:2111621,76,76,,,696886025,607737206,605609129,699045963,2111621,SRX3058780,SRS2404535,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.9089,0.91353,0.03824,0.03668,0.78261,0.78293,0.49562,0.49348,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48370,SRR5893068,SRX3058777,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.1,AG00730.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.1_R1.fastq.gz AG00730.1_R2.fastq.gz,fastq fastq,788630112.0,5188356.0,AG00730.1 R1.fastq.gz,0:76 1:76,A:241944426;C:145730020;G:152521090;T:246715939;N:1718637,76,76,,,241944426,145730020,152521090,246715939,1718637,SRX3058777,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.72997,0.66601,0.51477,0.46195,0.7611,0.77027,0.48262,0.48514,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48372,SRR5893070,SRX3058775,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.3,AG00730.3,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.3_R1.fastq.gz AG00730.3_R2.fastq.gz,fastq fastq,2381566704.0,15668202.0,AG00730.3 R2.fastq.gz,0:76 1:76,A:699742976;C:480758524;G:501871756;T:694897427;N:4296021,76,76,,,699742976,480758524,501871756,694897427,4296021,SRX3058775,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.64984,0.69686,0.44721,0.49461,0.77575,0.7558,0.49124,0.49296,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48373,SRR5893071,SRX3058774,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.2,AG00730.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.2_R1.fastq.gz AG00730.2_R2.fastq.gz,fastq fastq,2758536584.0,18148267.0,AG00730.2 R2.fastq.gz,0:76 1:76,A:819274018;C:547358767;G:578250069;T:813046584;N:607146,76,76,,,819274018,547358767,578250069,813046584,607146,SRX3058774,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.63895,0.70578,0.44175,0.50387,0.76844,0.74988,0.49353,0.49135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48375,SRR5893162,SRX3058683,SRS2404571,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am shield pA B1,dev timecourse AG00700,,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:9|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am shield pA B1,AG00700.1,AG00700.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00700.1_R1.fastq.gz AG00700.1_R2.fastq.gz,fastq fastq,2276298800.0,14975650.0,AG00700.1 R1.fastq.gz,0:76 1:76,A:608754452;C:529104329;G:527812421;T:608782771;N:1844827,76,76,,,608754452,529104329,527812421,608782771,1844827,SRX3058683,SRS2404571,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.91533,0.91935,0.03891,0.03686,0.78289,0.78281,0.49374,0.49427,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48376,SRR5893163,SRX3058682,SRS2404574,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield R0 B2,dev timecourse AG00685,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:6|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield R0 B2,AG00685.2,AG00685.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00685.2_R1.fastq.gz AG00685.2_R2.fastq.gz,fastq fastq,1680110568.0,11053359.0,AG00685.2 R2.fastq.gz,0:76 1:76,A:429590606;C:407853081;G:410551734;T:431833883;N:281264,76,76,,,429590606,407853081,410551734,431833883,281264,SRX3058682,SRS2404574,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.80758,0.77739,0.2587,0.25273,0.75162,0.75012,0.49289,0.48814,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48382,SRR5893169,SRX3058676,SRS2404578,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield R0 B1,dev timecourse AG00684,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:6|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield R0 B1,AG00684.1,AG00684.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00684.1_R2.fastq.gz AG00684.1_R1.fastq.gz,fastq fastq,2226499040.0,14648020.0,AG00684.1 R1.fastq.gz,0:76 1:76,A:602558683;C:513781901;G:511035245;T:594547415;N:4575796,76,76,,,602558683,513781901,511035245,594547415,4575796,SRX3058676,SRS2404578,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.8496,0.84272,0.25441,0.24624,0.7501,0.74838,0.47046,0.47693,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48383,SRR5893170,SRX3058675,SRS2404574,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield R0 B2,dev timecourse AG00685,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:6|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield R0 B2,AG00685.1,AG00685.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00685.1_R2.fastq.gz AG00685.1_R1.fastq.gz,fastq fastq,2296708448.0,15109924.0,AG00685.1 R1.fastq.gz,0:76 1:76,A:629149868;C:520713186;G:520261374;T:621870139;N:4713881,76,76,,,629149868,520713186,520261374,621870139,4713881,SRX3058675,SRS2404574,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84968,0.84234,0.28684,0.27563,0.74957,0.74667,0.47755,0.4838,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51332,SRR8784143,SRX5574148,SRS4536708,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h r2 B2,RESA   WT 6h r2 B2 AGN000587,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000532|replicate ref:AGN000587|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h r2 B2,AGR000770,AGR000770,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000770_R1.fastq.gz AGR000770_R2.fastq.gz,fastq fastq,710612768.0,4675084.0,AGR000770 R1.fastq.gz,0:76 1:76,A:216034520;C:140249508;G:140825200;T:212576797;N:926743,76,76,,,216034520,140249508,140825200,212576797,926743,SRX5574148,SRS4536708,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84791,0.85232,0.03648,0.0373,0.96992,0.96982,0.47482,0.48015,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51333,SRR8784144,SRX5574147,SRS4536708,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h r2 B2,RESA   WT 6h r2 B2 AGN000587,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000532|replicate ref:AGN000587|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h r2 B2,AGR000769,AGR000769,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000769_R1.fastq.gz AGR000769_R2.fastq.gz,fastq fastq,211548888.0,1391769.0,AGR000769 R1.fastq.gz,0:76 1:76,A:64102332;C:41963002;G:42116026;T:62997625;N:369903,76,76,,,64102332,41963002,42116026,62997625,369903,SRX5574147,SRS4536708,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84057,0.84101,0.03626,0.03615,0.96903,0.96924,0.47894,0.48212,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51335,SRR8784146,SRX5574145,SRS4536706,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h r2 B3,RESA   WT 6h r2 B3 AGN000591,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000532|replicate ref:AGN000591|replicate order:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h r2 B3,AGR000771,AGR000771,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000771_R1.fastq.gz AGR000771_R2.fastq.gz,fastq fastq,857903504.0,5644102.0,AGR000771 R1.fastq.gz,0:76 1:76,A:261246476;C:168915312;G:169170702;T:257095534;N:1475480,76,76,,,261246476,168915312,169170702,257095534,1475480,SRX5574145,SRS4536706,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84499,0.84594,0.0361,0.03624,0.96924,0.96954,0.48999,0.48378,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51338,SRR8784149,SRX5574142,SRS4536705,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h r2 B1,RESA   WT 6h r2 B1 AGN000582,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000532|replicate ref:AGN000582|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h r2 B1,AGR000768,AGR000768,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000768_R1.fastq.gz AGR000768_R2.fastq.gz,fastq fastq,970151856.0,6382578.0,AGR000768 R1.fastq.gz,0:76 1:76,A:294386849;C:192114485;G:192378258;T:289576859;N:1695405,76,76,,,294386849,192114485,192378258,289576859,1695405,SRX5574142,SRS4536705,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84582,0.84496,0.0368,0.03617,0.96857,0.96861,0.47723,0.46086,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51342,SRR8784153,SRX5574138,SRS4536691,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B2,RESA   WT 6h DL B2 AGN000464,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000464|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B2,AGR000589,AGR000589,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000589_R1.fastq.gz,fastq,561870964.0,7393039.0,AGR000589 R1.fastq.gz,0:76,A:166080691;C:147716691;G:133930960;T:114124874;N:17748,76,,,,166080691,147716691,133930960,114124874,17748,SRX5574138,SRS4536691,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.72489,,0.0602,,0.80144,,0.56469,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51343,SRR8784154,SRX5574137,SRS4536691,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B2,RESA   WT 6h DL B2 AGN000464,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000464|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B2,AGR000590,AGR000590,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000590_R1.fastq.gz,fastq,437266684.0,5753509.0,AGR000590 R1.fastq.gz,0:76,A:128941167;C:118340164;G:105849956;T:84119631;N:15766,76,,,,128941167,118340164,105849956,84119631,15766,SRX5574137,SRS4536691,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86075,,0.06544,,0.789,,0.5666,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51345,SRR8784156,SRX5574135,SRS4536702,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B1,RESA   WT 6h DL B1 AGN000463,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000463|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B1,AGR000586,AGR000586,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000586_R1.fastq.gz,fastq,2694327908.0,35451683.0,AGR000586 R1.fastq.gz,0:76,A:792570782;C:707468179;G:645543769;T:548410233;N:334945,76,,,,792570782,707468179,645543769,548410233,334945,SRX5574135,SRS4536702,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87772,,0.0691,,0.78253,,0.55589,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51346,SRR8784157,SRX5574134,SRS4536702,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B1,RESA   WT 6h DL B1 AGN000463,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000463|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B1,AGR000587,AGR000587,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000587_R1.fastq.gz,fastq,4527174612.0,59568087.0,AGR000587 R1.fastq.gz,0:76,A:1333909359;C:1198529946;G:1088707889;T:905780915;N:246503,76,,,,1333909359,1198529946,1088707889,905780915,246503,SRX5574134,SRS4536702,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.88145,,0.06801,,0.7821,,0.5579,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51347,SRR8784158,SRX5574133,SRS4536691,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B2,RESA   WT 6h DL B2 AGN000464,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000464|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B2,AGR000588,AGR000588,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000588_R1.fastq.gz,fastq,2583741068.0,33996593.0,AGR000588 R1.fastq.gz,0:76,A:764950474;C:674818484;G:613560780;T:530095680;N:315650,76,,,,764950474,674818484,613560780,530095680,315650,SRX5574133,SRS4536691,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87665,,0.0686,,0.78332,,0.55645,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51353,SRR8784164,SRX5574127,SRS4536698,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 8h a Am pA r3 B1,RESA   WT 8h a Am pA r3 B1 AGN001062,,strain:TU/AB|age:8|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|selection:pA|sample ref:AGS000941|replicate ref:AGN001062|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 8h a Am pA r3 B1,AGR001457,AGR001457,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR001457_R1.fastq.gz AGR001457_R2.fastq.gz,fastq fastq,1091406664.0,7180307.0,AGR001457 R1.fastq.gz,0:76 1:76,A:338277626;C:209601360;G:211052818;T:332448031;N:26829,76,76,,,338277626,209601360,211052818,332448031,26829,SRX5574127,SRS4536698,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.843,0.84316,0.03591,0.03493,0.97133,0.97074,0.47855,0.47491,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51362,SRR8784173,SRX5574118,SRS4536691,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 6h DL B2,RESA   WT 6h DL B2 AGN000464,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000443|replicate ref:AGN000464|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 6h DL B2,AGR000591,AGR000591,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR000591_R1.fastq.gz,fastq,441977544.0,5815494.0,AGR000591 R1.fastq.gz,0:76,A:126131136;C:119386206;G:107561398;T:88889359;N:9445,76,,,,126131136,119386206,107561398,88889359,9445,SRX5574118,SRS4536691,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.71586,,0.05415,,0.80113,,0.56621,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51372,SRR8784183,SRX5574108,SRS4536689,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 8h a Am pA r3 B3,RESA   WT 8h a Am pA r3 B3 AGN001064,,strain:TU/AB|age:8|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|selection:pA|sample ref:AGS000941|replicate ref:AGN001064|replicate order:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 8h a Am pA r3 B3,AGR001459,AGR001459,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR001459_R1.fastq.gz AGR001459_R2.fastq.gz,fastq fastq,1466122688.0,9645544.0,AGR001459 R1.fastq.gz,0:76 1:76,A:455341747;C:280749005;G:282302377;T:447692059;N:37500,76,76,,,455341747,280749005,282302377,447692059,37500,SRX5574108,SRS4536689,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84266,0.84348,0.03662,0.0361,0.97232,0.97218,0.46974,0.47375,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51373,SRR8784184,SRX5574107,SRS4536686,SRP189389,PRJNA528980,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA,PRJNA528980,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.,,,,RESA   WT 8h a Am pA r3 B2,RESA   WT 8h a Am pA r3 B2 AGN001063,,strain:TU/AB|age:8|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|selection:pA|sample ref:AGS000941|replicate ref:AGN001063|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA   WT 8h a Am pA r3 B2,AGR001458,AGR001458,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189389,,,AGR001458_R1.fastq.gz AGR001458_R2.fastq.gz,fastq fastq,728165424.0,4790562.0,AGR001458 R1.fastq.gz,0:76 1:76,A:225801650;C:139760608;G:140579216;T:222005064;N:18886,76,76,,,225801650,139760608,140579216,222005064,18886,SRX5574107,SRS4536686,SRA865803,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84582,0.845,0.03593,0.03495,0.9713,0.97189,0.47034,0.47028,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51484,SRR8787683,SRX5577525,SRS4539452,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 6h patA B1,iCLIP   iC celf1 6h patA B1 AGN001503,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:iCLIP pateamineA|molecule:RNA|selection:FLAG antibody|sample ref:AGS001052|replicate ref:AGN001503|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 6h patA B1,AGR001799,AGR001799,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001799_R1.fastq.gz,fastq,446788113.0,11250077.0,AGR001799 R1.fastq.gz,0:39.71 1:0,A:106747420;C:95157711;G:126230107;T:118614135;N:38740,39,0,,,106747420,95157711,126230107,118614135,38740,SRX5577525,SRS4539452,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.2838,,0.09711,,0.88982,,0.56274,,45,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51490,SRR8787689,SRX5577519,SRS4539448,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 6h patA B3,iCLIP   iC celf1 6h patA B3 AGN001505,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:iCLIP pateamineA|molecule:RNA|selection:FLAG antibody|sample ref:AGS001052|replicate ref:AGN001505|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 6h patA B3,AGR001801,AGR001801,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001801_R1.fastq.gz,fastq,1152834833.0,29378629.0,AGR001801 R1.fastq.gz,0:39.24 1:0,A:285052637;C:234325512;G:331753379;T:301601843;N:101462,39,0,,,285052637,234325512,331753379,301601843,101462,SRX5577519,SRS4539448,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.36834,,0.14603,,0.85825,,0.5349,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51491,SRR8787690,SRX5577518,SRS4539447,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 6h patA B2,iCLIP   iC celf1 6h patA B2 AGN001504,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:iCLIP pateamineA|molecule:RNA|selection:FLAG antibody|sample ref:AGS001052|replicate ref:AGN001504|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 6h patA B2,AGR001800,AGR001800,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001800_R1.fastq.gz,fastq,270825178.0,6973483.0,AGR001800 R1.fastq.gz,0:38.84 1:0,A:62608071;C:48467554;G:72166187;T:87559128;N:24238,38,0,,,62608071,48467554,72166187,87559128,24238,SRX5577518,SRS4539447,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.44004,,0.15223,,0.88296,,0.48489,,41,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51604,SRR8787803,SRX5577405,SRS4539383,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,Raw multiplex: iCLIP celf1 6h patA B1;iCLIP celf1 6h patA B2;iCLIP celf1 6h patA B3,Raw multiplex: iC celf1 6h patA B1 AGN001503;iC celf1 6h patA B2 AGN001504;iC celf1 6h patA B3 AGN001505,,strain:TU/AB|age:6|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:iCLIP pateamineA|molecule:RNA|selection:FLAG antibody|sample ref:AGS001052|replicate ref:AGN001503;AGN001504;AGN001505|replicate order:1;2;3|barcode:AGAG;CACA;TCTC|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: iCLIP celf1 6h patA B1;iCLIP celf1 6h patA B2;iCLIP celf1 6h patA B3,AGR001799;AGR001800;AGR001801,AGR001799;AGR001800;AGR001801,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,HWM5VADXX_celf6h_004_R1.fastq.gz,fastq,5950664264.0,78298214.0,HWM5VADXX celf6h 004 R1.fastq.gz,0:76,A:1652737986;C:1478775208;G:1460211004;T:1358226052;N:714014,76,,,,1652737986,1478775208,1460211004,1358226052,714014,SRX5577405,SRS4539383,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0011,,0.00048,,0.99801,,0.57391,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51629,SRR8788640,SRX5578483,SRS4540267,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield pA,Developmental timecourse   WT TinyLNA430 shield pA AGN000727,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:pA|sample ref:AGS000618|replicate ref:AGN000727|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield pA,AGR000971,AGR000971,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000971_R1.fastq.gz AGR000971_R2.fastq.gz,fastq fastq,2688437832.0,17687091.0,AGR000971 R1.fastq.gz,0:76 1:76,A:734926506;C:610335608;G:606492984;T:734578783;N:2103951,76,76,,,734926506,610335608,606492984,734578783,2103951,SRX5578483,SRS4540267,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.91779,0.922,0.07881,0.07629,0.75239,0.75227,0.47786,0.48583,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51643,SRR8788654,SRX5578469,SRS4540255,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi R0 B1,Developmental timecourse   WT 75%epi R0 B1 AGN000686,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000595|replicate ref:AGN000686|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi R0 B1,AGR000895,AGR000895,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000895_R1.fastq.gz AGR000895_R2.fastq.gz,fastq fastq,2102166080.0,13830040.0,AGR000895 R1.fastq.gz,0:76 1:76,A:623252641;C:414639301;G:435666345;T:624815002;N:3792791,76,76,,,623252641,414639301,435666345,624815002,3792791,SRX5578469,SRS4540255,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.72192,0.65038,0.5345,0.46896,0.75998,0.78119,0.48017,0.47887,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51644,SRR8788655,SRX5578468,SRS4540232,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi R0 B2,Developmental timecourse   WT 75%epi R0 B2 AGN000687,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000595|replicate ref:AGN000687|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi R0 B2,AGR000896,AGR000896,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000896_R1.fastq.gz AGR000896_R2.fastq.gz,fastq fastq,1141885712.0,7512406.0,AGR000896 R1.fastq.gz,0:76 1:76,A:353906338;C:210112438;G:219648296;T:355865932;N:2352708,76,76,,,353906338,210112438,219648296,355865932,2352708,SRX5578468,SRS4540232,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.78107,0.70975,0.61022,0.54702,0.74677,0.76165,0.50515,0.50274,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51645,SRR8788656,SRX5578467,SRS4540255,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi R0 B1,Developmental timecourse   WT 75%epi R0 B1 AGN000686,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000595|replicate ref:AGN000686|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi R0 B1,AGR000893,AGR000893,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000893_R2.fastq.gz AGR000893_R1.fastq.gz,fastq fastq,1977815488.0,13011944.0,AGR000893 R1.fastq.gz,0:76 1:76,A:603782849;C:366971866;G:386914613;T:615992169;N:4153991,76,76,,,603782849,366971866,386914613,615992169,4153991,SRX5578467,SRS4540255,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.75506,0.66718,0.56267,0.48988,0.76019,0.77559,0.4802,0.47867,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51646,SRR8788657,SRX5578466,SRS4540255,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi R0 B1,Developmental timecourse   WT 75%epi R0 B1 AGN000686,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000595|replicate ref:AGN000686|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi R0 B1,AGR000894,AGR000894,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000894_R1.fastq.gz AGR000894_R2.fastq.gz,fastq fastq,2482381008.0,16331454.0,AGR000894 R1.fastq.gz,0:76 1:76,A:742190641;C:483444680;G:513170162;T:743281889;N:293636,76,76,,,742190641,483444680,513170162,743281889,293636,SRX5578466,SRS4540255,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.72582,0.63678,0.54042,0.46184,0.7528,0.7752,0.48229,0.48184,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51649,SRR8788660,SRX5578463,SRS4540252,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi pA B1,Developmental timecourse   WT 75%epi pA B1 AGN000660,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000582|replicate ref:AGN000660|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi pA B1,AGR000852,AGR000852,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000852_R1.fastq.gz AGR000852_R2.fastq.gz,fastq fastq,2691158632.0,17704991.0,AGR000852 R1.fastq.gz,0:76 1:76,A:733547947;C:612852820;G:609796735;T:732612584;N:2348546,76,76,,,733547947,612852820,609796735,732612584,2348546,SRX5578463,SRS4540252,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.92547,0.92861,0.09837,0.09653,0.7539,0.75392,0.48469,0.47698,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51650,SRR8788661,SRX5578462,SRS4540251,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi pA B2,Developmental timecourse   WT 75%epi pA B2 AGN000661,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000582|replicate ref:AGN000661|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi pA B2,AGR000853,AGR000853,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000853_R1.fastq.gz AGR000853_R2.fastq.gz,fastq fastq,2771867288.0,18235969.0,AGR000853 R1.fastq.gz,0:76 1:76,A:751378839;C:635357530;G:633122574;T:749604126;N:2404219,76,76,,,751378839,635357530,633122574,749604126,2404219,SRX5578462,SRS4540251,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.92544,0.93146,0.08321,0.0818,0.75459,0.75465,0.47826,0.47521,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51651,SRR8788662,SRX5578461,SRS4540250,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 50%epi pA B1,Developmental timecourse   WT 50%epi pA B1 AGN000656,,strain:TU/AB|age:5.3|dev stage:50% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000580|replicate ref:AGN000656|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 50%epi pA B1,AGR000848,AGR000848,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000848_R1.fastq.gz AGR000848_R2.fastq.gz,fastq fastq,2659268728.0,17495189.0,AGR000848 R1.fastq.gz,0:76 1:76,A:729090922;C:600236639;G:601406532;T:725733628;N:2801007,76,76,,,729090922,600236639,601406532,725733628,2801007,SRX5578461,SRS4540250,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93054,0.934,0.07811,0.07599,0.75233,0.75276,0.49215,0.48908,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51652,SRR8788663,SRX5578460,SRS4540249,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 50%epi pA B2,Developmental timecourse   WT 50%epi pA B2 AGN000657,,strain:TU/AB|age:5.3|dev stage:50% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000580|replicate ref:AGN000657|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 50%epi pA B2,AGR000849,AGR000849,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000849_R1.fastq.gz AGR000849_R2.fastq.gz,fastq fastq,2341487496.0,15404523.0,AGR000849 R1.fastq.gz,0:76 1:76,A:628561357;C:543152397;G:540289309;T:627048357;N:2436076,76,76,,,628561357,543152397,540289309,627048357,2436076,SRX5578460,SRS4540249,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93911,0.94113,0.07246,0.07019,0.75035,0.75059,0.47206,0.47943,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51670,SRR8788681,SRX5578442,SRS4540235,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am 75%epi pA B1,Developmental timecourse   WT a Am 75%epi pA B1 AGN000702,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|sample ref:AGS000603|replicate ref:AGN000702|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am 75%epi pA B1,AGR000914,AGR000914,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000914_R1.fastq.gz AGR000914_R2.fastq.gz,fastq fastq,2508564680.0,16503715.0,AGR000914 R1.fastq.gz,0:76 1:76,A:675596035;C:576942832;G:576325266;T:677693685;N:2006862,76,76,,,675596035,576942832,576325266,677693685,2006862,SRX5578442,SRS4540235,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.90791,0.91175,0.0427,0.04023,0.79553,0.79472,0.49443,0.49817,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51677,SRR8788688,SRX5578435,SRS4540232,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 75%epi R0 B2,Developmental timecourse   WT 75%epi R0 B2 AGN000687,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000595|replicate ref:AGN000687|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 75%epi R0 B2,AGR000897,AGR000897,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000897_R1.fastq.gz AGR000897_R2.fastq.gz,fastq fastq,1455605808.0,9576354.0,AGR000897 R1.fastq.gz,0:76 1:76,A:445117856;C:276577736;G:288276887;T:445397980;N:235349,76,76,,,445117856,276577736,288276887,445397980,235349,SRX5578435,SRS4540232,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.75358,0.66566,0.59107,0.50634,0.74813,0.76928,0.50336,0.50373,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51688,SRR8788699,SRX5578424,SRS4540221,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 50%epi R0 B1,Developmental timecourse   WT 50%epi R0 B1 AGN000682,,strain:TU/AB|age:5.3|dev stage:50% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000593|replicate ref:AGN000682|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 50%epi R0 B1,AGR000887,AGR000887,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000887_R1.fastq.gz AGR000887_R2.fastq.gz,fastq fastq,2215475544.0,14575497.0,AGR000887 R1.fastq.gz,0:76 1:76,A:604719775;C:505332541;G:503482415;T:597466501;N:4474312,76,76,,,604719775,505332541,503482415,597466501,4474312,SRX5578424,SRS4540221,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84896,0.84508,0.26997,0.26237,0.74381,0.7428,0.47551,0.47832,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51690,SRR8788701,SRX5578422,SRS4540223,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 50%epi R0 B2,Developmental timecourse   WT 50%epi R0 B2 AGN000683,,strain:TU/AB|age:5.3|dev stage:50% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000593|replicate ref:AGN000683|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 50%epi R0 B2,AGR000889,AGR000889,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000889_R1.fastq.gz AGR000889_R2.fastq.gz,fastq fastq,1324409744.0,8713222.0,AGR000889 R1.fastq.gz,0:76 1:76,A:356402847;C:307410596;G:305516843;T:352458081;N:2621377,76,76,,,356402847,307410596,305516843,352458081,2621377,SRX5578422,SRS4540223,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.84928,0.84353,0.22237,0.21602,0.74026,0.73817,0.46957,0.47137,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51691,SRR8788702,SRX5578421,SRS4540221,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT 50%epi R0 B1,Developmental timecourse   WT 50%epi R0 B1 AGN000682,,strain:TU/AB|age:5.3|dev stage:50% epiboly|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000593|replicate ref:AGN000682|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 50%epi R0 B1,AGR000888,AGR000888,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000888_R1.fastq.gz AGR000888_R2.fastq.gz,fastq fastq,2431710744.0,15998097.0,AGR000888 R1.fastq.gz,0:76 1:76,A:601964902;C:611028930;G:612007692;T:606311353;N:397867,76,76,,,601964902,611028930,612007692,606311353,397867,SRX5578421,SRS4540221,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.75793,0.79917,0.23052,0.24009,0.74821,0.75156,0.49174,0.49921,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51697,SRR8788708,SRX5578415,SRS4540216,SRP189512,PRJNA529241,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse,PRJNA529241,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am 75%epi pA B2,Developmental timecourse   WT a Am 75%epi pA B2 AGN000703,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|sample ref:AGS000603|replicate ref:AGN000703|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am 75%epi pA B2,AGR000915,AGR000915,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP189512,,,AGR000915_R1.fastq.gz AGR000915_R2.fastq.gz,fastq fastq,2115163904.0,13915552.0,AGR000915 R1.fastq.gz,0:76 1:76,A:568499415;C:487947770;G:488248426;T:568760760;N:1707533,76,76,,,568499415,487947770,488248426,568760760,1707533,SRX5578415,SRS4540216,SRA866166,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.87166,0.8805,0.04612,0.04264,0.79744,0.7974,0.50588,0.50613,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-05-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62489,SRR13234605,SRX9666721,SRS7865658,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf triptolide ribo0,MZythdf2 vs bkgd match WT mRNA pA &amp; R0  rep1   MZythdf2 6h trip r0 AGN001795,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2  8/ 8|strain maternal:ythdf2  8/ 8|strain paternal:ythdf2  8/ 8|treatment:triptolide|molecule:mRNA|selection:r0|sample ref:AGS001441|replicate ref:AGN001795|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf triptolide ribo0,AGR002455,AGR002455,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP297464,,,AGR002455_R1.fastq.gz,fastq,2342992220.0,30828845.0,AGR002455 R1.fastq.gz,0:76 1:0,A:486939172;C:667467813;G:688508751;T:499974142;N:102342,76,0,,,486939172,667467813,688508751,499974142,102342,SRX9666721,SRS7865658,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.49109,,0.13387,,0.79304,,0.50899,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62490,SRR13234606,SRX9666720,SRS7865657,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   MZdicer 6hpf shield polyA,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA &amp; R0   MZdicer 6h shield pA AGN000135,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer  / |strain paternal:dicer  / |molecule:RNA|selection:pA|sample ref:AGS000123|replicate ref:AGN000135|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   MZdicer 6hpf shield polyA,AGR000189,AGR000189,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP297464,,,AGR000189_R1.fastq.gz,fastq,3092161992.0,40686342.0,AGR000189 R1.fastq.gz,0:76 1:0,A:843616790;C:685315432;G:677129339;T:885937873;N:162558,76,0,,,843616790,685315432,677129339,885937873,162558,SRX9666720,SRS7865657,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.93709,,0.13352,,0.75363,,0.48096,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62491,SRR13234607,SRX9666719,SRS7865656,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   background matched wild type 6hpf untreated ribo0,MZythdf2 vs bkgd match WT mRNA pA &amp; R0  rep1   bkgd match WT 6h r0 AGN001794,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+  or +/   or  / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:r0|sample ref:AGS001440|replicate ref:AGN001794|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   background matched wild type 6hpf untreated ribo0,AGR002454,AGR002454,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP297464,,,AGR002454_R1.fastq.gz,fastq,2427554532.0,31941507.0,AGR002454 R1.fastq.gz,0:76 1:0,A:522620648;C:658233071;G:668206211;T:578388551;N:106051,76,0,,,522620648,658233071,668206211,578388551,106051,SRX9666719,SRS7865656,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.63583,,0.17863,,0.76861,,0.50012,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62492,SRR13234608,SRX9666718,SRS7865655,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf untreated ribo0,MZythdf2 vs bkgd match WT mRNA pA &amp; R0  rep1   MZythdf2 6h r0 AGN001793,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2  8/ 8|strain maternal:ythdf2  8/ 8|strain paternal:ythdf2  8/ 8|molecule:mRNA|selection:r0|sample ref:AGS001439|replicate ref:AGN001793|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf untreated ribo0,AGR002453,AGR002453,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP297464,,,AGR002453_R1.fastq.gz,fastq,2027694820.0,26680195.0,AGR002453 R1.fastq.gz,0:76 1:0,A:419274134;C:549004017;G:566872772;T:492455226;N:88671,76,0,,,419274134,549004017,566872772,492455226,88671,SRX9666718,SRS7865655,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.61548,,0.17157,,0.76986,,0.47549,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62498,SRR13234614,SRX9666712,SRS7865649,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   background matched wild type 6hpf triptolide polyA,MZythdf2 vs bkgd match WT mRNA pA &amp; R0  rep1   bkgd match WT 6h trip pA AGN001786,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+  or +/   or  / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001432|replicate ref:AGN001786|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   background matched wild type 6hpf triptolide polyA,AGR002446,AGR002446,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP297464,,,AGR002446_R1.fastq.gz,fastq,1124283808.0,14793208.0,AGR002446 R1.fastq.gz,0:76 1:0,A:303085193;C:262065829;G:254422392;T:304661911;N:48483,76,0,,,303085193,262065829,254422392,304661911,48483,SRX9666712,SRS7865649,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.90758,,0.10149,,0.75298,,0.50822,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-09,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62499,SRR13234615,SRX9666711,SRS7865646,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf triptolide polyA,MZythdf2 vs bkgd match WT mRNA pA &amp; R0  rep1   MZythdf2 6h trip pA AGN001785,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2  8/ 8|strain maternal:ythdf2  8/ 8|strain paternal:ythdf2  8/ 8|treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001431|replicate ref:AGN001785|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,MZythdf2 vs bkgd match WT mRNA pA & R0  rep1   MZythdf2 6hpf triptolide polyA,AGR002445,AGR002445,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP297464,,,AGR002445_R1.fastq.gz,fastq,982349780.0,12925655.0,AGR002445 R1.fastq.gz,0:76 1:0,A:263625214;C:224164362;G:222612457;T:271905809;N:41938,76,0,,,263625214,224164362,222612457,271905809,41938,SRX9666711,SRS7865646,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.90172,,0.10357,,0.75621,,0.50493,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-09,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62501,SRR13234617,SRX9666709,SRS7865647,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type 6hpf shield + U1U2 morpholino polyA,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA &amp; R0   WT 6h shield U1U2 MO pA AGN000134,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:U1U2 morpholino|molecule:RNA|selection:pA|sample ref:AGS000122|replicate ref:AGN000134|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type 6hpf shield + U1U2 morpholino polyA,AGR000188,AGR000188,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP297464,,,AGR000188_R1.fastq.gz,fastq,2315635336.0,30468886.0,AGR000188 R1.fastq.gz,0:76 1:0,A:650669894;C:502589633;G:490937822;T:670879962;N:558025,76,0,,,650669894,502589633,490937822,670879962,558025,SRX9666709,SRS7865647,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.91636,,0.26406,,0.78709,,0.51247,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62512,SRR13234628,SRX9666698,SRS7865636,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type 6hpf shield + alpha amanitin + miR 430 polyA,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA &amp; R0   WT 6h shield a Am miR 430 pA AGN000133,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:alpha amanitin miR 430|molecule:RNA|selection:pA|sample ref:AGS000121|replicate ref:AGN000133|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type 6hpf shield + alpha amanitin + miR 430 polyA,AGR000187,AGR000187,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP297464,,,AGR000187_R1.fastq.gz,fastq,2631852716.0,34629641.0,AGR000187 R1.fastq.gz,0:76 1:0,A:694722114;C:608051504;G:592006258;T:736477995;N:594845,76,0,,,694722114,608051504,592006258,736477995,594845,SRX9666698,SRS7865636,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94914,,0.0523,,0.79001,,0.49444,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62518,SRR13234634,SRX9666692,SRS7865630,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   MZdrosha 6hpf shield + miR 430 polyA,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA &amp; R0   MZdrosha 6h shield miR 430 pA AGN000146,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha  / |strain paternal:drosha  / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000134|replicate ref:AGN000146|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   MZdrosha 6hpf shield + miR 430 polyA,AGR000200,AGR000200,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP297464,,,AGR000200_R1.fastq.gz,fastq,3919751224.0,51575674.0,AGR000200 R1.fastq.gz,0:76 1:0,A:1081009237;C:874549155;G:855765442;T:1108099190;N:328200,76,0,,,1081009237,874549155,855765442,1108099190,328200,SRX9666692,SRS7865630,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.94118,,0.10939,,0.74878,,0.4731,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
62519,SRR13234635,SRX9666691,SRS7865626,SRP297464,PRJNA683902,Ythdf m6A readers function redundantly during zebrafish development,PRJNA683902,Other,During the maternal to zygotic transition MZT  multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay  yet how this modification promotes maternal transcript degradation remains unclear. Here  we find that m6A promotes maternal mRNA deadenylation. Yet  genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance  zygotic genome activation  or the onset of gastrulation  challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development  as double Ythdf2 and Ythdf3 deletion prevented female gonad formation  and triple Ythdf mutants were lethal. Finally  we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation  and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type + tinyLNA miR 430 6hpf shield ribo0,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA &amp; R0   WT tinyLNA miR 430 6h shield r0 AGN000145,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:tinyLNA for miR 430|molecule:RNA|selection:r0|sample ref:AGS000133|replicate ref:AGN000145|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,WT  MZdrosha  MZdicer mRNA 6  24  48 hpf  pA & R0   wild type + tinyLNA miR 430 6hpf shield ribo0,AGR000199,AGR000199,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP297464,,,AGR000199_R1.fastq.gz,fastq,3973389592.0,52281442.0,AGR000199 R1.fastq.gz,0:76 1:0,A:732379950;C:1180161072;G:1218688247;T:841847667;N:312656,76,0,,,732379950,1180161072,1218688247,841847667,312656,SRX9666691,SRS7865626,SRA1169659,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.66604,,0.19006,,0.78289,,0.48187,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-12-10,Gastrula,Embryo,Embryo Imprecise,All anatomical structures