rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
36407,SRR546818,SRX180748,SRS347209,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage,D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,,,,,,,,,,,RNAseq   D. rerio dome/zfs:0000015 embryo,RNAseq   D. rerio dome/zfs:0000015 embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_30p_dome_1.fastq,fastq,2359648608.0,15524004.0,RNAseq   D. rerio dome/zfs:0000015 embryo,0:76 1:76,A:588562906;C:575605218;G:603310130;T:589755481;N:2414873,76,76,,,588562906,575605218,603310130,589755481,2414873,SRX180748,SRS347209,SRA055273,University of Bergen,ZEPROME consortium,2,0.89779,0.9222,0.04122,0.0431,0.76609,0.77112,0.49779,0.49305,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40724,SRR3420333,SRX1660350,SRS1360304,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.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 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,,,AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz,fastq fastq,2314408088.0,15226369.0,AG00715 run 1,0:76 1:76,A:652783335;C:485705748;G:507451689;T:663544778;N:4922538,76,76,,,652783335,485705748,507451689,663544778,4922538,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59859,0.55293,0.24175,0.21943,0.78384,0.79174,0.52173,0.52111,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40725,SRR3420337,SRX1660350,SRS1360304,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.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 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,,,AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz,fastq fastq,2461668424.0,16195187.0,AG00715 run 2,0:76 1:76,A:653884256;C:562168304;G:597853484;T:647470498;N:291882,76,76,,,653884256,562168304,597853484,647470498,291882,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.5374,0.51402,0.2167,0.19427,0.78575,0.7934,0.52714,0.53043,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40726,SRR3420341,SRX1660350,SRS1360304,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.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 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,,,AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz,fastq fastq,3692351624.0,24291787.0,AG00715 run 3,0:76 1:76,A:984283909;C:835828915;G:881112020;T:975490829;N:15635951,76,76,,,984283909,835828915,881112020,975490829,15635951,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.54752,0.52404,0.18037,0.16908,0.79358,0.7961,0.50982,0.50975,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40727,SRR3420346,SRX1660346,SRS1360308,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.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 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,,,AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz,fastq fastq,2377192296.0,15639423.0,AG00714 run 1,0:76 1:76,A:694380135;C:473427723;G:496920379;T:707435115;N:5028944,76,76,,,694380135,473427723,496920379,707435115,5028944,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.69444,0.63521,0.40011,0.36148,0.76252,0.77116,0.50751,0.5108,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40728,SRR3420349,SRX1660346,SRS1360308,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.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 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,,,AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz,fastq fastq,1841902256.0,12117778.0,AG00714 run 2,0:76 1:76,A:517451432;C:392444197;G:415696773;T:508506741;N:7803113,76,76,,,517451432,392444197,415696773,508506741,7803113,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63625,0.60304,0.3341,0.31189,0.77224,0.77703,0.50754,0.51039,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40729,SRR3420359,SRX1660342,SRS1360312,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.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 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,,,AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz,fastq fastq,2674764976.0,17597138.0,AG00713 run 1,0:76 1:76,A:738399424;C:560443522;G:578733188;T:791450319;N:5738523,76,76,,,738399424,560443522,578733188,791450319,5738523,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63595,0.60509,0.17579,0.17695,0.79066,0.79815,0.49657,0.4916,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40730,SRR3420362,SRX1660342,SRS1360312,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.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 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,,,AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz,fastq fastq,2463895376.0,16209838.0,AG00713 run 2,0:76 1:76,A:661360403;C:556078326;G:581335469;T:654625128;N:10496050,76,76,,,661360403,556078326,581335469,654625128,10496050,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.58767,0.56878,0.14864,0.14485,0.79476,0.79898,0.49508,0.49769,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40731,SRR3420369,SRX1660341,SRS1360313,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.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 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,,,AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz,fastq fastq,1354427464.0,8910707.0,AG00712 run 1,0:76 1:76,A:382647488;C:281900295;G:291990859;T:395032379;N:2856443,76,76,,,382647488,281900295,291990859,395032379,2856443,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.64156,0.60052,0.23835,0.22296,0.78025,0.78717,0.49813,0.49898,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40732,SRR3420375,SRX1660341,SRS1360313,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.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 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,,,AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz,fastq fastq,2335782480.0,15366990.0,AG00712 run 2,0:76 1:76,A:638971995;C:517112038;G:538588809;T:640731763;N:377875,76,76,,,638971995,517112038,538588809,640731763,377875,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60525,0.56571,0.24772,0.21069,0.77043,0.78543,0.50862,0.50386,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40733,SRR3420379,SRX1660340,SRS1360314,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.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 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,,,AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz,fastq fastq,2343343264.0,15416732.0,AG00711 run 1,0:76 1:76,A:645206414;C:505367235;G:523792864;T:663977432;N:4999319,76,76,,,645206414,505367235,523792864,663977432,4999319,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59395,0.56211,0.10259,0.10243,0.80598,0.80911,0.51352,0.53772,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40734,SRR3420383,SRX1660340,SRS1360314,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.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 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,,,AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz,fastq fastq,2668460776.0,17555663.0,AG00711 run 2,0:76 1:76,A:709820753;C:602900273;G:626554840;T:717828006;N:11356904,76,76,,,709820753,602900273,626554840,717828006,11356904,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.56281,0.54232,0.09217,0.09047,0.80657,0.81018,0.50757,0.52507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40735,SRR3420304,SRX1660339,SRS1360299,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.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 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,,,AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz,fastq fastq,2705199784.0,17797367.0,AG00710 run 1,0:76 1:76,A:737065338;C:573787464;G:595216660;T:793361986;N:5768336,76,76,,,737065338,573787464,595216660,793361986,5768336,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60426,0.58122,0.08196,0.09224,0.80578,0.8075,0.50121,0.50121,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40736,SRR3420308,SRX1660339,SRS1360299,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.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 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,,,AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz,fastq fastq,2275540168.0,14970659.0,AG00710 run 2,0:76 1:76,A:614429428;C:505827101;G:528906356;T:616697803;N:9679480,76,76,,,614429428,505827101,528906356,616697803,9679480,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.57792,0.56382,0.07268,0.07246,0.80261,0.80612,0.49743,0.50296,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
41388,SRR4375300,SRX2226793,SRS1732685,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA CLIP Ago2   RESA CLIP Ago2 input,resa clip ago2 AG01631,,strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:5% input before pulldown|condition:input|BioSampleModel:Model organism or animal,,,,,,,,,RESA CLIP Ago2   RESA CLIP Ago2 input,AG01631.1,AG01631.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz,fastq fastq,9864834960.0,64900230.0,AG01631.1 R2.fastq.gz,0:76 1:76,A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520,76,76,,,2990534603,1958949912,1963153108,2951932817,264520,SRX2226793,SRS1732685,SRA482696,Yale University|Genetics,Yale University,2,0.83121,0.85078,0.03505,0.0364,0.97171,0.97019,0.46925,0.47246,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
41389,SRR4375299,SRX2226779,SRS1732684,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA CLIP Ago2   RESA CLIP Ago2 IP,resa clip ago2 AG01630,,strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:flag bead pulldown post crosslinking|condition:Ago2 IP|BioSampleModel:Model organism or animal,,,,,,,,,RESA CLIP Ago2   RESA CLIP Ago2 IP,AG01630.1,AG01630.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz,fastq fastq,9348207632.0,61501366.0,AG01630.1 R1.fastq.gz,0:76 1:76,A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848,76,76,,,2819572908,1871537719,1881735941,2775115216,245848,SRX2226779,SRS1732684,SRA482696,Yale University|Genetics,Yale University,2,0.80207,0.78648,0.02992,0.02839,0.97885,0.97871,0.49297,0.49107,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43058,SRR8354695,SRX5165478,SRS4174524,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 1,DMS seq   RNA positives ctrl in vitro B1 AG01489,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 1,AG01489.1,AG01489.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01489.1_R1.fastq.gz,fastq,75703530.0,2718404.0,AG01489.1 R1.fastq.gz,0:27.85 1:0,A:18206335;C:19464567;G:21319876;T:16712584;N:168,27,0,,,18206335,19464567,21319876,16712584,168,SRX5165478,SRS4174524,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02389,,0.00591,,0.97654,,0.4758,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43059,SRR8354696,SRX5165477,SRS4174523,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 2,DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 2,AG01490.1,AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01490.1_R1.fastq.gz,fastq,295051199.0,10869746.0,AG01490.1 R1.fastq.gz,0:27.14 1:0,A:71900468;C:76519029;G:81589099;T:65042019;N:584,27,0,,,71900468,76519029,81589099,65042019,584,SRX5165477,SRS4174523,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02362,,0.00528,,0.98173,,0.35096,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43060,SRR8354697,SRX5165476,SRS4174522,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,Raw multiplex: DMS seq   RNA positives ctrl in vitro B1 AG01489;DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,AG01489.1;AG01490.1,AG01489.1;AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MYYANXX_JBDX127_009_R1.fastq.gz,fastq,1115150128.0,14673028.0,C7MYYANXX JBDX127 009 R1.fastq.gz,0:76,A:313482382;C:276309346;G:291633361;T:233659719;N:65320,76,,,,313482382,276309346,291633361,233659719,65320,SRX5165476,SRS4174522,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00546,,0.00047,,0.98602,,0.51535,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43111,SRR5893078,SRX3058767,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.6,AG01043.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.6_R1.fastq.gz,fastq,245591088.0,10387582.0,AG01043.6 R1.fastq.gz,0:23.64 1:0,A:66848740;C:56927652;G:60996703;T:60816631;N:1362,23,0,,,66848740,56927652,60996703,60816631,1362,SRX3058767,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62265,,0.12438,,0.7696,,0.59474,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43112,SRR5893079,SRX3058766,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.5,AG01043.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.5_R1.fastq.gz,fastq,935516222.0,39234795.0,AG01043.5 R1.fastq.gz,0:23.84 1:0,A:254864411;C:216185186;G:231676738;T:232716892;N:72995,23,0,,,254864411,216185186,231676738,232716892,72995,SRX3058766,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.6326,,0.12713,,0.76739,,0.59812,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43113,SRR5893080,SRX3058765,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.4,AG01043.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.4_R1.fastq.gz,fastq,633932186.0,26698352.0,AG01043.4 R1.fastq.gz,0:23.74 1:0,A:172078766;C:147459021;G:157655737;T:156729321;N:9341,23,0,,,172078766,147459021,157655737,156729321,9341,SRX3058765,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62892,,0.12689,,0.76915,,0.59625,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43114,SRR5893081,SRX3058764,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.3,AG01043.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.3_R1.fastq.gz,fastq,545501906.0,22980935.0,AG01043.3 R1.fastq.gz,0:23.74 1:0,A:147643154;C:127194084;G:135926112;T:134737007;N:1549,23,0,,,147643154,127194084,135926112,134737007,1549,SRX3058764,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.63069,,0.12544,,0.76781,,0.60018,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43125,SRR5893092,SRX3058753,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.1,AG01043.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.1_R1.fastq.gz,fastq,108747256.0,4575669.0,AG01043.1 R1.fastq.gz,0:23.77 1:0,A:29414532;C:25366431;G:27139739;T:26826074;N:480,23,0,,,29414532,25366431,27139739,26826074,480,SRX3058753,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62913,,0.12566,,0.76946,,0.59653,,20,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43126,SRR5893093,SRX3058752,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.2,AG01043.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.2_R1.fastq.gz,fastq,37331204.0,1581621.0,AG01043.2 R1.fastq.gz,0:23.60 1:0,A:10098397;C:8686566;G:9362492;T:9181793;N:1956,23,0,,,10098397,8686566,9362492,9181793,1956,SRX3058752,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60497,,0.12042,,0.77114,,0.5559,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43145,SRR5893112,SRX3058733,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.4,AG01049.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.4_R1.fastq.gz,fastq,693084196.0,30220927.0,AG01049.4 R1.fastq.gz,0:22.93 1:0,A:184260362;C:156379835;G:169790720;T:182650190;N:3089,22,0,,,184260362,156379835,169790720,182650190,3089,SRX3058733,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56552,,0.10478,,0.77329,,0.58948,,15,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43146,SRR5893113,SRX3058732,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.3,AG01049.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.3_R1.fastq.gz,fastq,605892767.0,26434367.0,AG01049.3 R1.fastq.gz,0:22.92 1:0,A:160713810;C:136961096;G:148749325;T:159466624;N:1912,22,0,,,160713810,136961096,148749325,159466624,1912,SRX3058732,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.5625,,0.10811,,0.77224,,0.58777,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43147,SRR5893114,SRX3058731,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.6,AG01049.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.6_R1.fastq.gz,fastq,394478885.0,17274979.0,AG01049.6 R1.fastq.gz,0:22.84 1:0,A:105227778;C:88892938;G:96681477;T:103674703;N:1989,22,0,,,105227778,88892938,96681477,103674703,1989,SRX3058731,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.55998,,0.10523,,0.77279,,0.58664,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43148,SRR5893115,SRX3058730,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.5,AG01049.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.5_R1.fastq.gz,fastq,886753255.0,38566196.0,AG01049.5 R1.fastq.gz,0:22.99 1:0,A:235539511;C:199422326;G:217573523;T:234156689;N:61206,22,0,,,235539511,199422326,217573523,234156689,61206,SRX3058730,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56676,,0.10782,,0.77331,,0.58475,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43151,SRR5893118,SRX3058727,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.2,AG01049.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.2_R1.fastq.gz,fastq,37381210.0,1641906.0,AG01049.2 R1.fastq.gz,0:22.77 1:0,A:9910821;C:8448316;G:9246060;T:9775054;N:959,22,0,,,9910821,8448316,9246060,9775054,959,SRX3058727,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.54348,,0.10292,,0.77467,,0.59127,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43152,SRR5893119,SRX3058726,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.1,AG01049.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.1_R1.fastq.gz,fastq,113060119.0,4927027.0,AG01049.1 R1.fastq.gz,0:22.95 1:0,A:29961989;C:25583869;G:27802427;T:29711326;N:508,22,0,,,29961989,25583869,27802427,29711326,508,SRX3058726,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56357,,0.10878,,0.77143,,0.59024,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48357,SRR5893043,SRX3058802,SRS2404516,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 1Kc R0 B1,dev timecourse AG00674,,strain:TU/AB|age:3.0|dev stage:1Kc|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:5|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 1Kc R0 B1,AG00674.1,AG00674.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00674.1_R1.fastq.gz AG00674.1_R2.fastq.gz,fastq fastq,2778354192.0,18278646.0,AG00674.1 R1.fastq.gz,0:76 1:76,A:714760759;C:677314739;G:673805073;T:706600617;N:5873004,76,76,,,714760759,677314739,673805073,706600617,5873004,SRX3058802,SRS2404516,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.86999,0.85982,0.06795,0.06797,0.7625,0.7615,0.47908,0.47887,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48360,SRR5893046,SRX3058799,SRS2404519,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 sphere pA B1,dev timecourse AG00652,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:2|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT sphere pA B1,AG00652.1,AG00652.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00652.1_R1.fastq.gz AG00652.1_R2.fastq.gz,fastq fastq,2249814472.0,14801411.0,AG00652.1 R2.fastq.gz,0:76 1:76,A:601647003;C:522830587;G:520544682;T:602476586;N:2315614,76,76,,,601647003,522830587,520544682,602476586,2315614,SRX3058799,SRS2404519,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94297,0.93993,0.04239,0.0447,0.74627,0.74651,0.48492,0.48304,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2017-08-03,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48361,SRR5893047,SRX3058798,SRS2404518,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 sphere pA B2,dev timecourse AG00653,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:2|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT sphere pA B2,AG00653.1,AG00653.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00653.1_R1.fastq.gz AG00653.1_R2.fastq.gz,fastq fastq,2426358520.0,15962885.0,AG00653.1 R2.fastq.gz,0:76 1:76,A:652817175;C:559502193;G:558238114;T:653277750;N:2523288,76,76,,,652817175,559502193,558238114,653277750,2523288,SRX3058798,SRS2404518,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93982,0.9342,0.0439,0.04618,0.74823,0.74777,0.48614,0.48263,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48368,SRR5893066,SRX3058779,SRS2404534,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 1Kc R0 B1,dev timecourse AG00729,,strain:TU/AB|age:3.0|dev stage:1Kc|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:11|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 1Kc R0 B1,AG00729.1,AG00729.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00729.1_R1.fastq.gz AG00729.1_R2.fastq.gz,fastq fastq,1890136872.0,12435111.0,AG00729.1 R1.fastq.gz,0:76 1:76,A:533950687;C:392378762;G:409763231;T:549817692;N:4226500,76,76,,,533950687,392378762,409763231,549817692,4226500,SRX3058779,SRS2404534,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.63533,0.59715,0.26221,0.24377,0.76924,0.77303,0.49119,0.4915,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48371,SRR5893069,SRX3058776,SRS2404534,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 1Kc R0 B1,dev timecourse AG00729,,strain:TU/AB|age:3.0|dev stage:1Kc|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:11|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 1Kc R0 B1,AG00729.2,AG00729.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00729.2_R1.fastq.gz AG00729.2_R2.fastq.gz,fastq fastq,2313466600.0,15220175.0,AG00729.2 R1.fastq.gz,0:76 1:76,A:629795330;C:513868215;G:540304279;T:629131946;N:366830,76,76,,,629795330,513868215,540304279,629131946,366830,SRX3058776,SRS2404534,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.58985,0.55361,0.25806,0.21955,0.76593,0.7791,0.49969,0.49044,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48374,SRR5893161,SRX3058684,SRS2404573,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 sphere pA B2,dev timecourse AG00699,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:8|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am sphere pA B2,AG00699.1,AG00699.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00699.1_R1.fastq.gz AG00699.1_R2.fastq.gz,fastq fastq,3068083672.0,20184761.0,AG00699.1 R2.fastq.gz,0:76 1:76,A:815949630;C:716718414;G:714252482;T:818688450;N:2474696,76,76,,,815949630,716718414,714252482,818688450,2474696,SRX3058684,SRS2404573,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93448,0.93065,0.02663,0.02862,0.76577,0.76597,0.48311,0.48106,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48379,SRR5893166,SRX3058679,SRS2404576,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 sphere pA B1,dev timecourse AG00698,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:8|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am sphere pA B1,AG00698.1,AG00698.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00698.1_R1.fastq.gz AG00698.1_R2.fastq.gz,fastq fastq,3080491584.0,20266392.0,AG00698.1 R2.fastq.gz,0:76 1:76,A:820145004;C:719352396;G:717040476;T:821459264;N:2494444,76,76,,,820145004,719352396,717040476,821459264,2494444,SRX3058679,SRS2404576,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93863,0.93287,0.02829,0.03003,0.76674,0.76613,0.48947,0.48528,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48380,SRR5893167,SRX3058678,SRS2404577,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 1Kc R0 B2,dev timecourse AG00675,,strain:TU/AB|age:3.0|dev stage:1Kc|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:5|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 1Kc R0 B2,AG00675.1,AG00675.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00675.1_R1.fastq.gz AG00675.1_R2.fastq.gz,fastq fastq,2036894544.0,13400622.0,AG00675.1 R1.fastq.gz,0:76 1:76,A:518808025;C:503536266;G:498902325;T:511311573;N:4336355,76,76,,,518808025,503536266,498902325,511311573,4336355,SRX3058678,SRS2404577,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.8614,0.84624,0.07306,0.07361,0.76621,0.7651,0.48141,0.47999,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48381,SRR5893168,SRX3058677,SRS2404577,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 1Kc R0 B2,dev timecourse AG00675,,strain:TU/AB|age:3.0|dev stage:1Kc|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:5|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 1Kc R0 B2,AG00675.2,AG00675.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00675.2_R1.fastq.gz AG00675.2_R2.fastq.gz,fastq fastq,2783867992.0,18314921.0,AG00675.2 R1.fastq.gz,0:76 1:76,A:638343367;C:750975688;G:753870541;T:640053360;N:625036,76,76,,,638343367,750975688,753870541,640053360,625036,SRX3058677,SRS2404577,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.73502,0.78624,0.07089,0.0748,0.76865,0.76999,0.48242,0.48382,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48384,SRR7236655,SRX4142917,SRS3356704,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B2 AG01175;KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01175.2;AG01176.2,AG01175.2;AG01176.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLV3ADXX_kh2_NOBCX_R1.fastq.gz,fastq,7675050912.0,100987512.0,HHLV3ADXX kh2 NOBCX R1.fastq.gz,0:76,A:2241934669;C:1774343310;G:1727825603;T:1912212373;N:18734957,76,,,,2241934669,1774343310,1727825603,1912212373,18734957,SRX4142917,SRS3356704,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00123,,0.00083,,0.99939,,0.47297,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48385,SRR7236656,SRX4142916,SRS3356704,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B2 AG01175;KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01175.1;AG01176.1,AG01175.1;AG01176.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLY2ADXX_kh2_NOBCX_R1.fastq.gz,fastq,10199922760.0,134209510.0,HHLY2ADXX kh2 NOBCX R1.fastq.gz,0:76,A:2990232290;C:2350693064;G:2293777949;T:2554099449;N:11120008,76,,,,2990232290,2350693064,2293777949,2554099449,11120008,SRX4142916,SRS3356704,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00128,,0.00076,,0.99945,,0.43877,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48386,SRR7236657,SRX4142915,SRS3356703,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,Raw multiplex: KHSRP iCLIP   iC Khsrp noAb B3 AG01177;KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:;KHSRP antibody|replicate group:2;1|replicate:3|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01177.2;AG01178.2,AG01177.2;AG01178.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLTFADXX_kh3_022_R1.fastq.gz,fastq,5612942988.0,73854513.0,HHLTFADXX kh3 022 R1.fastq.gz,0:76,A:1761182916;C:1273000548;G:1339715056;T:1238748082;N:296386,76,,,,1761182916,1273000548,1339715056,1238748082,296386,SRX4142915,SRS3356703,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00125,,0.00069,,0.99831,,0.5566,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48387,SRR7236658,SRX4142914,SRS3356703,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,Raw multiplex: KHSRP iCLIP   iC Khsrp noAb B3 AG01177;KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:;KHSRP antibody|replicate group:2;1|replicate:3|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01177.1;AG01178.1,AG01177.1;AG01178.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLV3ADXX_kh3_NOBCX_R1.fastq.gz,fastq,7810653532.0,102771757.0,HHLV3ADXX kh3 NOBCX R1.fastq.gz,0:76,A:2439317937;C:1775190292;G:1863760875;T:1714265680;N:18118748,76,,,,2439317937,1775190292,1863760875,1714265680,18118748,SRX4142914,SRS3356703,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00121,,0.00071,,0.99864,,0.54444,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48388,SRR7236659,SRX4142913,SRS3356702,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:3|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01178.2,AG01178.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01178.2_R1.fastq.gz,fastq,1046051929.0,35061189.0,AG01178.2 R1.fastq.gz,0:29.84 1:0,A:304629557;C:170568838;G:208541597;T:362307791;N:4146,29,0,,,304629557,170568838,208541597,362307791,4146,SRX4142913,SRS3356702,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.68324,,0.4824,,0.78139,,0.51734,,20,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48389,SRR7236660,SRX4142912,SRS3356702,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:3|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01178.1,AG01178.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01178.1_R1.fastq.gz,fastq,1429865561.0,47958542.0,AG01178.1 R1.fastq.gz,0:29.81 1:0,A:416462367;C:233529708;G:285810572;T:494062288;N:626,29,0,,,416462367,233529708,285810572,494062288,626,SRX4142912,SRS3356702,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67776,,0.47933,,0.782,,0.52337,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48390,SRR7236661,SRX4142911,SRS3356701,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B1 AG01173;KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:1|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01173.2;AG01174.2,AG01173.2;AG01174.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHMMTADXX_kh1_020_R1.fastq.gz,fastq,5281915868.0,69498893.0,HHMMTADXX kh1 020 R1.fastq.gz,0:76,A:1639173476;C:1196546385;G:1285461861;T:1160482436;N:251710,76,,,,1639173476,1196546385,1285461861,1160482436,251710,SRX4142911,SRS3356701,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00021,,0.00011,,0.99973,,0.64705,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48391,SRR7236662,SRX4142910,SRS3356701,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B1 AG01173;KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:1|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01173.1;AG01174.1,AG01173.1;AG01174.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLY2ADXX_kh1_NOBCX_R1.fastq.gz,fastq,9991920032.0,131472632.0,HHLY2ADXX kh1 NOBCX R1.fastq.gz,0:76,A:3100849614;C:2254998457;G:2420727161;T:2205131206;N:10213594,76,,,,3100849614,2254998457,2420727161,2205131206,10213594,SRX4142910,SRS3356701,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00019,,0.0001,,0.99975,,0.46666,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48392,SRR7236663,SRX4142909,SRS3356700,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,KHSRP iCLIP   iC Khsrp noAb B3 AG01177,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,AG01177.2,AG01177.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01177.2_R1.fastq.gz,fastq,885888031.0,33497952.0,AG01177.2 R1.fastq.gz,0:26.45 1:0,A:206425913;C:174763971;G:243957147;T:260737810;N:3190,26,0,,,206425913,174763971,243957147,260737810,3190,SRX4142909,SRS3356700,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.06832,,0.02459,,0.98098,,0.60923,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48393,SRR7236664,SRX4142908,SRS3356700,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,KHSRP iCLIP   iC Khsrp noAb B3 AG01177,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,AG01177.1,AG01177.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01177.1_R1.fastq.gz,fastq,1222226291.0,46319107.0,AG01177.1 R1.fastq.gz,0:26.39 1:0,A:284330952;C:241163311;G:337366164;T:359365256;N:608,26,0,,,284330952,241163311,337366164,359365256,608,SRX4142908,SRS3356700,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.06321,,0.02496,,0.99541,,0.59566,,24,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48394,SRR7236665,SRX4142907,SRS3356699,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01176.2,AG01176.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01176.2_R1.fastq.gz,fastq,233885454.0,7281208.0,AG01176.2 R1.fastq.gz,0:32.12 1:0,A:54788902;C:54168846;G:66577250;T:58350443;N:13,32,0,,,54788902,54168846,66577250,58350443,13,SRX4142907,SRS3356699,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.10795,,0.04438,,0.97516,,0.69327,,38,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48395,SRR7236666,SRX4142906,SRS3356699,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01176.1,AG01176.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01176.1_R1.fastq.gz,fastq,311212095.0,9672607.0,AG01176.1 R1.fastq.gz,0:32.17 1:0,A:73018762;C:72027124;G:88456228;T:77709256;N:725,32,0,,,73018762,72027124,88456228,77709256,725,SRX4142906,SRS3356699,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.10719,,0.04462,,0.97498,,0.70725,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48396,SRR7236667,SRX4142905,SRS3356698,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,KHSRP iCLIP   iC Khsrp Ab B2 AG01175,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:2|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,AG01175.2,AG01175.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01175.2_R1.fastq.gz,fastq,2466162835.0,77779195.0,AG01175.2 R1.fastq.gz,0:31.71 1:0,A:716944933;C:413092452;G:514707831;T:821417411;N:208,31,0,,,716944933,413092452,514707831,821417411,208,SRX4142905,SRS3356698,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.64577,,0.4225,,0.77516,,0.52286,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48397,SRR7236668,SRX4142904,SRS3356698,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,KHSRP iCLIP   iC Khsrp Ab B2 AG01175,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:2|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,AG01175.1,AG01175.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01175.1_R1.fastq.gz,fastq,3316001149.0,104496257.0,AG01175.1 R1.fastq.gz,0:31.73 1:0,A:964563720;C:554605513;G:690144862;T:1106678088;N:8966,31,0,,,964563720,554605513,690144862,1106678088,8966,SRX4142904,SRS3356698,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.64794,,0.42598,,0.77719,,0.53602,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48398,SRR7236669,SRX4142903,SRS3356697,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01174.2,AG01174.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01174.2_R1.fastq.gz,fastq,997707611.0,35501164.0,AG01174.2 R1.fastq.gz,0:28.10 1:0,A:234873124;C:200942687;G:273279747;T:288611385;N:668,28,0,,,234873124,200942687,273279747,288611385,668,SRX4142903,SRS3356697,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.05803,,0.02195,,0.99632,,0.62645,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48399,SRR7236670,SRX4142902,SRS3356697,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01174.1,AG01174.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01174.1_R1.fastq.gz,fastq,1864739454.0,66313666.0,AG01174.1 R1.fastq.gz,0:28.12 1:0,A:439206469;C:375517297;G:509810941;T:540192256;N:12491,28,0,,,439206469,375517297,509810941,540192256,12491,SRX4142902,SRS3356697,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0573,,0.02132,,0.99618,,0.52433,,34,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48400,SRR7236671,SRX4142901,SRS3356696,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,KHSRP iCLIP   iC Khsrp Ab B1 AG01173,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,AG01173.2,AG01173.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01173.2_R1.fastq.gz,fastq,867830730.0,28259963.0,AG01173.2 R1.fastq.gz,0:30.71 1:0,A:248512374;C:137460842;G:175204067;T:306652878;N:569,30,0,,,248512374,137460842,175204067,306652878,569,SRX4142901,SRS3356696,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67622,,0.4515,,0.76765,,0.52978,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48401,SRR7236672,SRX4142900,SRS3356696,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key 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 endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,KHSRP iCLIP   iC Khsrp Ab B1 AG01173,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,AG01173.1,AG01173.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01173.1_R1.fastq.gz,fastq,1644979798.0,53548650.0,AG01173.1 R1.fastq.gz,0:30.72 1:0,A:471457103;C:259804358;G:331035207;T:582672297;N:10833,30,0,,,471457103,259804358,331035207,582672297,10833,SRX4142900,SRS3356696,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67964,,0.45484,,0.77147,,0.52736,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51148,SRR8552540,SRX5354350,SRS4345568,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 4h,ClickIT pulldown RNA seq   WT 4h CiT AGN001955,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|condition:untreated|sample ref:AGS001551|replicate ref:AGN001955|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 4h,AGR002639,AGR002639,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002639_R1.fastq.gz,fastq,669823264.0,8813464.0,AGR002639 R1.fastq.gz,0:76,A:180580309;C:156267879;G:146882617;T:186073903;N:18556,76,,,,180580309,156267879,146882617,186073903,18556,SRX5354350,SRS4345568,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.79799,,0.4317,,0.80107,,0.49938,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51149,SRR8552541,SRX5354349,SRS4345567,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with Triptolide treatment at 1Kc rep2,ClickIT pulldown RNA seq   1Kc trip CiT B2 AGN001948,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:triptolide|molecule:RNA|selection:click it|sample ref:AGS001546|replicate ref:AGN001948|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with Triptolide treatment at 1Kc rep2,AGR002632,AGR002632,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002632_R1.fastq.gz,fastq,736209188.0,9686963.0,AGR002632 R1.fastq.gz,0:76,A:170587459;C:201745745;G:181888662;T:181967760;N:19562,76,,,,170587459,201745745,181888662,181967760,19562,SRX5354349,SRS4345567,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.8577,,0.22956,,0.88686,,0.84725,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51150,SRR8552542,SRX5354348,SRS4345566,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with Triptolide treatment at 1Kc rep1,ClickIT pulldown RNA seq   1Kc trip CiT B1 AGN001947,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:triptolide|molecule:RNA|selection:click it|sample ref:AGS001546|replicate ref:AGN001947|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with Triptolide treatment at 1Kc rep1,AGR002631,AGR002631,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002631_R1.fastq.gz,fastq,581513848.0,7651498.0,AGR002631 R1.fastq.gz,0:76,A:135989486;C:160445990;G:142966504;T:142096430;N:15438,76,,,,135989486,160445990,142966504,142096430,15438,SRX5354348,SRS4345566,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85088,,0.2219,,0.89453,,0.83092,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51151,SRR8552543,SRX5354347,SRS4345565,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc rep2,ClickIT pulldown RNA seq   WT 1Kc CiT B2 AGN001944,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|condition:untreated|sample ref:AGS001544|replicate ref:AGN001944|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc rep2,AGR002628,AGR002628,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002628_R1.fastq.gz,fastq,659665256.0,8679806.0,AGR002628 R1.fastq.gz,0:76,A:165695429;C:169324267;G:156643240;T:167984494;N:17826,76,,,,165695429,169324267,156643240,167984494,17826,SRX5354347,SRS4345565,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82849,,0.35512,,0.83307,,0.76885,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51154,SRR8552546,SRX5354344,SRS4345562,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,mRNA seq   WT 4h R0,mRNA seq   WT 4h R0 AGN001743,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|condition:untreated|sample ref:AGS001389|replicate ref:AGN001743|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq   WT 4h R0,AGR002398,AGR002398,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002398_R1.fastq.gz,fastq,1304401604.0,17163179.0,AGR002398 R1.fastq.gz,0:76,A:248973263;C:385894356;G:377042802;T:292460281;N:30902,76,,,,248973263,385894356,377042802,292460281,30902,SRX5354344,SRS4345562,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82485,,0.15823,,0.78847,,0.75023,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51156,SRR8552548,SRX5354342,SRS4345560,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with jq1 treatment at 4h,ClickIT pulldown RNA seq   4h jq1 CiT AGN001957,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:jq1|molecule:RNA|selection:click it|sample ref:AGS001553|replicate ref:AGN001957|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with jq1 treatment at 4h,AGR002641,AGR002641,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002641_R1.fastq.gz,fastq,617341464.0,8122914.0,AGR002641 R1.fastq.gz,0:76,A:145459477;C:161070486;G:148779348;T:162015070;N:17083,76,,,,145459477,161070486,148779348,162015070,17083,SRX5354342,SRS4345560,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84995,,0.36631,,0.83475,,0.73425,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51157,SRR8552549,SRX5354341,SRS4345559,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with triptolide treatment at 4h,ClickIT pulldown RNA seq   4h trip CiT AGN001956,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:triptolide|molecule:RNA|selection:click it|sample ref:AGS001552|replicate ref:AGN001956|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with triptolide treatment at 4h,AGR002640,AGR002640,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002640_R1.fastq.gz,fastq,667446516.0,8782191.0,AGR002640 R1.fastq.gz,0:76,A:165899174;C:163852470;G:156648205;T:181028079;N:18588,76,,,,165899174,163852470,156648205,181028079,18588,SRX5354341,SRS4345559,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87239,,0.32295,,0.82337,,0.79526,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51158,SRR8552550,SRX5354340,SRS4345558,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c collected at 4h momC rep2,ClickIT pulldown RNA seq   WT 4h patA CHX@8c CiT mC B2 AGN002004,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX PatA|molecule:RNA|selection:click it|sample ref:AGS001574|replicate ref:AGN002004|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c collected at 4h momC rep2,AGR002688,AGR002688,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002688_R1.fastq.gz,fastq,899183436.0,11831361.0,AGR002688 R1.fastq.gz,0:76,A:208770903;C:231292869;G:218574665;T:240318959;N:226040,76,,,,208770903,231292869,218574665,240318959,226040,SRX5354340,SRS4345558,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84418,,0.15854,,0.90985,,0.83845,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51159,SRR8552551,SRX5354339,SRS4345557,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with p300 and brd4 collected at 4h momC rep1,ClickIT pulldown RNA seq   WT 4h patA CHX p300 brd4@8c CiT mC B1 AGN002005,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX PatA p300 brd4|molecule:RNA|selection:click it|sample ref:AGS001575|replicate ref:AGN002005|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with p300 and brd4 collected at 4h momC rep1,AGR002690,AGR002690,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002690_R1.fastq.gz,fastq,740259304.0,9740254.0,AGR002690 R1.fastq.gz,0:76,A:161212143;C:204928950;G:192052874;T:181874361;N:190976,76,,,,161212143,204928950,192052874,181874361,190976,SRX5354339,SRS4345557,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85997,,0.22335,,0.91427,,0.86061,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51160,SRR8552552,SRX5354338,SRS4345556,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with p300 and brd4 collected at 4h momC rep2,ClickIT pulldown RNA seq   WT 4h patA CHX p300 brd4@8c CiT mC B2 AGN002006,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX PatA p300 brd4|molecule:RNA|selection:click it|sample ref:AGS001575|replicate ref:AGN002006|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with p300 and brd4 collected at 4h momC rep2,AGR002689,AGR002689,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002689_R1.fastq.gz,fastq,777131768.0,10225418.0,AGR002689 R1.fastq.gz,0:76,A:166364392;C:218505779;G:203269271;T:188796362;N:195964,76,,,,166364392,218505779,203269271,188796362,195964,SRX5354338,SRS4345556,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87289,,0.28031,,0.91319,,0.82014,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51161,SRR8552553,SRX5354337,SRS4345555,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with aAm collected at 4h momC rep1,ClickIT pulldown RNA seq   WT 4h patA CHX aAm@8c CiT mC B1 AGN002007,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX patA alpha am|molecule:RNA|selection:click it|sample ref:AGS001576|replicate ref:AGN002007|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with aAm collected at 4h momC rep1,AGR002691,AGR002691,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002691_R1.fastq.gz,fastq,845939964.0,11130789.0,AGR002691 R1.fastq.gz,0:76,A:175187649;C:251071813;G:225247987;T:194218492;N:214023,76,,,,175187649,251071813,225247987,194218492,214023,SRX5354337,SRS4345555,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.8899,,0.34025,,0.92178,,0.82363,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51162,SRR8552554,SRX5354336,SRS4345554,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with aAm collected at 4h momC rep2,ClickIT pulldown RNA seq   WT 4h patA CHX aAm@8c CiT mC B2 AGN002008,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX patA alpha am|molecule:RNA|selection:click it|sample ref:AGS001576|replicate ref:AGN002008|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c with aAm collected at 4h momC rep2,AGR002692,AGR002692,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002692_R1.fastq.gz,fastq,856575328.0,11270728.0,AGR002692 R1.fastq.gz,0:76,A:196407472;C:223854275;G:211503561;T:224594414;N:215606,76,,,,196407472,223854275,211503561,224594414,215606,SRX5354336,SRS4345554,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85442,,0.18048,,0.92042,,0.87941,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51163,SRR8552555,SRX5354335,SRS4345553,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c collected at 4h momD,ClickIT pulldown RNA seq   WT 4h patA CHX@32c CiT mD AGN002009,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX patA|molecule:RNA|selection:click it|sample ref:AGS001583|replicate ref:AGN002009|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c collected at 4h momD,AGR002705,AGR002705,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002705_R1.fastq.gz,fastq,812076112.0,10685212.0,AGR002705 R1.fastq.gz,0:76,A:203422465;C:198364460;G:187561230;T:222522645;N:205312,76,,,,203422465,198364460,187561230,222522645,205312,SRX5354335,SRS4345553,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82565,,0.3058,,0.81722,,0.79281,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51164,SRR8552556,SRX5354334,SRS4345552,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c with p300 and brd4 collected at 4h momD,ClickIT pulldown RNA seq   WT 4h patA CHX p300 brd4@32c CiT mD AGN002010,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX patA p300 brd4|molecule:RNA|selection:click it|sample ref:AGS001584|replicate ref:AGN002010|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c with p300 and brd4 collected at 4h momD,AGR002706,AGR002706,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002706_R1.fastq.gz,fastq,796037528.0,10474178.0,AGR002706 R1.fastq.gz,0:76,A:213105930;C:182101327;G:175043919;T:225583206;N:203146,76,,,,213105930,182101327,175043919,225583206,203146,SRX5354334,SRS4345552,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.81048,,0.41164,,0.78117,,0.56172,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51165,SRR8552557,SRX5354333,SRS4345551,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c with aAm collected at 4h momD,ClickIT pulldown RNA seq   WT 4h patA CHX aAm@32c CiT mD AGN002011,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX patA alpha am|molecule:RNA|selection:click it|sample ref:AGS001585|replicate ref:AGN002011|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 32c with aAm collected at 4h momD,AGR002707,AGR002707,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002707_R1.fastq.gz,fastq,916378132.0,12057607.0,AGR002707 R1.fastq.gz,0:76,A:196522099;C:258434234;G:240563187;T:220628967;N:229645,76,,,,196522099,258434234,240563187,220628967,229645,SRX5354333,SRS4345551,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86913,,0.26183,,0.91293,,0.83948,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51166,SRR8552558,SRX5354332,SRS4345550,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   1N 512c CiT,ClickIT pulldown RNA seq chk1 haploid   1N 512c CiT AGN002108,,strain:TU/AB|age:2.75|dev stage:512 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|sample ref:AGS001629|replicate ref:AGN002108|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   1N 512c CiT,AGR002792,AGR002792,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002792_R1.fastq.gz,fastq,386966844.0,5091669.0,AGR002792 R1.fastq.gz,0:76,A:93369497;C:99726289;G:94365818;T:99485751;N:19489,76,,,,93369497,99726289,94365818,99485751,19489,SRX5354332,SRS4345550,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82437,,0.23405,,0.86939,,0.85545,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51167,SRR8552559,SRX5354331,SRS4345549,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   1N a Am 512c CiT,ClickIT pulldown RNA seq chk1 haploid   1N a Am 512c CiT AGN002109,,strain:TU/AB|age:2.75|dev stage:512 cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:click it|sample ref:AGS001630|replicate ref:AGN002109|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   1N a Am 512c CiT,AGR002793,AGR002793,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002793_R1.fastq.gz,fastq,417628360.0,5495110.0,AGR002793 R1.fastq.gz,0:76,A:83566911;C:125200766;G:114437291;T:94402339;N:21053,76,,,,83566911,125200766,114437291,94402339,21053,SRX5354331,SRS4345549,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87248,,0.16951,,0.93754,,0.85694,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51168,SRR8552560,SRX5354330,SRS4345548,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c collected at 4h momC rep1,ClickIT pulldown RNA seq   WT 4h patA CHX@8c CiT mC B1 AGN002003,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:CHX PatA|molecule:RNA|selection:click it|sample ref:AGS001574|replicate ref:AGN002003|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with patA and CHX treatment at 8c collected at 4h momC rep1,AGR002687,AGR002687,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002687_R1.fastq.gz,fastq,885226796.0,11647721.0,AGR002687 R1.fastq.gz,0:76,A:207997932;C:221701573;G:210921495;T:244381469;N:224327,76,,,,207997932,221701573,210921495,244381469,224327,SRX5354330,SRS4345548,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85742,,0.13768,,0.91281,,0.80695,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51169,SRR8552561,SRX5354329,SRS4345547,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with aAm treatment at 1Kc momA rep2,ClickIT pulldown RNA seq   WT aAm 1Kc CiT mA B2 AGN002002,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:click it|sample ref:AGS001573|replicate ref:AGN002002|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with aAm treatment at 1Kc momA rep2,AGR002685,AGR002685,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002685_R1.fastq.gz,fastq,878247640.0,11555890.0,AGR002685 R1.fastq.gz,0:76,A:204180433;C:221942779;G:216189667;T:235714418;N:220343,76,,,,204180433,221942779,216189667,235714418,220343,SRX5354329,SRS4345547,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84991,,0.15021,,0.9051,,0.79006,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51170,SRR8552562,SRX5354328,SRS4345546,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with p300  BRD4 treatment at 1Kc momA rep1,ClickIT pulldown RNA seq   1Kc p300 brd4 CiT mA B1 AGN001999,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:p300 brd4|molecule:RNA|selection:click it|sample ref:AGS001572|replicate ref:AGN001999|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with p300  BRD4 treatment at 1Kc momA rep1,AGR002684,AGR002684,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002684_R1.fastq.gz,fastq,909960388.0,11973163.0,AGR002684 R1.fastq.gz,0:76,A:233271328;C:223286151;G:209773353;T:243402384;N:227172,76,,,,233271328,223286151,209773353,243402384,227172,SRX5354328,SRS4345546,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.81762,,0.4064,,0.79508,,0.72465,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51171,SRR8552563,SRX5354327,SRS4345545,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc mom A rep2,ClickIT pulldown RNA seq   WT 1Kc CiT mA B2 AGN001998,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|condition:untreated|sample ref:AGS001571|replicate ref:AGN001998|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc mom A rep2,AGR002682,AGR002682,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002682_R1.fastq.gz,fastq,913836996.0,12024171.0,AGR002682 R1.fastq.gz,0:76,A:221642600;C:235918255;G:221720215;T:234322678;N:233248,76,,,,221642600,235918255,221720215,234322678,233248,SRX5354327,SRS4345545,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.81645,,0.32525,,0.83305,,0.76673,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51172,SRR8552564,SRX5354326,SRS4345544,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with aAm treatment at 1Kc momA rep1,ClickIT pulldown RNA seq   WT aAm 1Kc CiT mA B1 AGN002001,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:click it|sample ref:AGS001573|replicate ref:AGN002001|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with aAm treatment at 1Kc momA rep1,AGR002686,AGR002686,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002686_R1.fastq.gz,fastq,820010816.0,10789616.0,AGR002686 R1.fastq.gz,0:76,A:162577457;C:244679720;G:229797634;T:182748376;N:207629,76,,,,162577457,244679720,229797634,182748376,207629,SRX5354326,SRS4345544,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.88608,,0.19401,,0.93874,,0.88162,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51173,SRR8552565,SRX5354325,SRS4345543,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with p300  BRD4 treatment at 1Kc momA rep2,ClickIT pulldown RNA seq   1Kc p300 brd4 CiT mA B2 AGN002000,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|treatment:p300 brd4|molecule:RNA|selection:click it|sample ref:AGS001572|replicate ref:AGN002000|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with p300  BRD4 treatment at 1Kc momA rep2,AGR002683,AGR002683,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002683_R1.fastq.gz,fastq,1128571804.0,14849629.0,AGR002683 R1.fastq.gz,0:76,A:278279990;C:286827626;G:268233040;T:294944931;N:286217,76,,,,278279990,286827626,268233040,294944931,286217,SRX5354325,SRS4345543,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.81077,,0.37877,,0.80316,,0.74386,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51175,SRR8552567,SRX5354323,SRS4345541,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with sgc treatment at 4h,ClickIT pulldown RNA seq   4h sgc CiT AGN001958,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:sgc|molecule:RNA|selection:click it|sample ref:AGS001554|replicate ref:AGN001958|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT with sgc treatment at 4h,AGR002642,AGR002642,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002642_R1.fastq.gz,fastq,633029688.0,8329338.0,AGR002642 R1.fastq.gz,0:76,A:148941680;C:163030095;G:151190225;T:169850585;N:17103,76,,,,148941680,163030095,151190225,169850585,17103,SRX5354323,SRS4345541,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84199,,0.36537,,0.82485,,0.70069,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51176,SRR8552568,SRX5354322,SRS4345540,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc mom A rep1,ClickIT pulldown RNA seq   WT 1Kc CiT mA B1 AGN001997,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|condition:untreated|sample ref:AGS001571|replicate ref:AGN001997|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq   ClickIT pulldown WT at 1Kc mom A rep1,AGR002681,AGR002681,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002681_R1.fastq.gz,fastq,757441080.0,9966330.0,AGR002681 R1.fastq.gz,0:76,A:167082102;C:213677417;G:194803753;T:181686347;N:191461,76,,,,167082102,213677417,194803753,181686347,191461,SRX5354322,SRS4345540,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86601,,0.36034,,0.86419,,0.735,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51178,SRR8552570,SRX5354320,SRS4345538,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   2N 1Kc CiT,ClickIT pulldown RNA seq chk1 haploid   2N 1Kc CiT AGN002113,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|sample ref:AGS001634|replicate ref:AGN002113|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   2N 1Kc CiT,AGR002797,AGR002797,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002797_R1.fastq.gz,fastq,803732680.0,10575430.0,AGR002797 R1.fastq.gz,0:76,A:201794657;C:198878293;G:186941049;T:216077418;N:41263,76,,,,201794657,198878293,186941049,216077418,41263,SRX5354320,SRS4345538,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.81296,,0.3091,,0.84116,,0.74082,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51179,SRR8552571,SRX5354319,SRS4345537,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   1N 1Kc CiT,ClickIT pulldown RNA seq chk1 haploid   1N 1Kc CiT AGN002112,,strain:TU/AB|age:3.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|sample ref:AGS001633|replicate ref:AGN002112|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   1N 1Kc CiT,AGR002796,AGR002796,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002796_R1.fastq.gz,fastq,722996132.0,9513107.0,AGR002796 R1.fastq.gz,0:76,A:192440181;C:175871393;G:169495763;T:185151987;N:36808,76,,,,192440181,175871393,169495763,185151987,36808,SRX5354319,SRS4345537,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.64494,,0.23214,,0.86468,,0.7057,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-02-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51180,SRR8552572,SRX5354318,SRS4345536,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   2N a Am 512c CiT,ClickIT pulldown RNA seq chk1 haploid   2N a Am 512c CiT AGN002111,,strain:TU/AB|age:2.75|dev stage:512 cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:click it|sample ref:AGS001632|replicate ref:AGN002111|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   2N a Am 512c CiT,AGR002795,AGR002795,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002795_R1.fastq.gz,fastq,853268720.0,11227220.0,AGR002795 R1.fastq.gz,0:76,A:219057982;C:211089842;G:208497142;T:214580524;N:43230,76,,,,219057982,211089842,208497142,214580524,43230,SRX5354318,SRS4345536,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.4962,,0.07741,,0.9388,,0.80683,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51181,SRR8552573,SRX5354317,SRS4345535,SRP184786,PRJNA521558,Brd4 and p300 confer transcriptional competency during zygotic genome activation,PRJNA521558,Other,The awakening of the genome post fertilization is a cornerstone of animal development. However  the mechanisms that activate the silent genome post fertilization are poorly understood. Here  we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus  is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these  the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked  whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.,,,,ClickIT pulldown RNA seq chk1 haploid   2N 512c CiT,ClickIT pulldown RNA seq chk1 haploid   2N 512c CiT AGN002110,,strain:TU/AB|age:2.75|dev stage:512 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:click it|sample ref:AGS001631|replicate ref:AGN002110|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,ClickIT pulldown RNA seq chk1 haploid   2N 512c CiT,AGR002794,AGR002794,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP184786,,,AGR002794_R1.fastq.gz,fastq,789837144.0,10392594.0,AGR002794 R1.fastq.gz,0:76,A:209027628;C:193947541;G:185420690;T:201401028;N:40257,76,,,,209027628,193947541,185420690,201401028,40257,SRX5354317,SRS4345535,SRA847217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.54493,,0.1913,,0.87986,,0.79852,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2019-06-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51374,SRR8787779,SRX5577635,SRS4539399,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 purbb B2,iCLIP   iC purbb B2 AGN001421,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001043|replicate ref:AGN001421|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP purbb B2,AGR001754,AGR001754,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001754_R1.fastq.gz,fastq,335887114.0,14991395.0,AGR001754 R1.fastq.gz,0:22.41 1:0,A:74180345;C:83232406;G:106310215;T:72164148;N:0,22,0,,,74180345,83232406,106310215,72164148,0,SRX5577635,SRS4539399,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.24414,,0.06603,,0.86592,,0.61809,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51375,SRR8787573,SRX5577634,SRS4539488,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 purbb B3,iCLIP   iC purbb B3 AGN001422,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001043|replicate ref:AGN001422|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP purbb B3,AGR001755,AGR001755,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001755_R1.fastq.gz,fastq,15677181.0,668468.0,AGR001755 R1.fastq.gz,0:23.45 1:0,A:4016903;C:3934951;G:4279760;T:3445518;N:49,23,0,,,4016903,3934951,4279760,3445518,49,SRX5577634,SRS4539488,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.19896,,0.05474,,0.89536,,0.6044,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51376,SRR8787574,SRX5577633,SRS4539386,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 hnrnpc B3,iCLIP   iC hnrnpc B3 AGN001322,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001029|replicate ref:AGN001322|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpc B3,AGR001650,AGR001650,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001650_R1.fastq.gz,fastq,629466824.0,18814705.0,AGR001650 R1.fastq.gz,0:33.46 1:0,A:156340325;C:132972003;G:151531068;T:188592616;N:30812,33,0,,,156340325,132972003,151531068,188592616,30812,SRX5577633,SRS4539386,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.49077,,0.31564,,0.92155,,0.52626,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51377,SRR8787575,SRX5577632,SRS4539496,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 hnrnpa0a B4,iCLIP   iC hnrnpa0a B4 AGN001314,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001314|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B4,AGR001634,AGR001634,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001634_R1.fastq.gz,fastq,906990390.0,29842065.0,AGR001634 R1.fastq.gz,0:30.39 1:0,A:217828894;C:216233390;G:248751189;T:224136392;N:40525,30,0,,,217828894,216233390,248751189,224136392,40525,SRX5577632,SRS4539496,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.17185,,0.10489,,0.93478,,0.59354,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51378,SRR8787576,SRX5577631,SRS4539496,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 hnrnpa0a B4,iCLIP   iC hnrnpa0a B4 AGN001314,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001314|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B4,AGR001633,AGR001633,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001633_R1.fastq.gz,fastq,372658652.0,12289936.0,AGR001633 R1.fastq.gz,0:30.32 1:0,A:89390910;C:89012247;G:102629829;T:91622338;N:3328,30,0,,,89390910,89012247,102629829,91622338,3328,SRX5577631,SRS4539496,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.1687,,0.10317,,0.93413,,0.61549,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51379,SRR8787577,SRX5577630,SRS4539495,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 hnrnpa0a B1,iCLIP   iC hnrnpa0a B1 AGN001182,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001182|replicate order:1|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B1,AGR001628,AGR001628,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001628_R1.fastq.gz,fastq,952894634.0,33140562.0,AGR001628 R1.fastq.gz,0:28.75 1:0,A:272894148;C:180655712;G:221297329;T:278047211;N:234,28,0,,,272894148,180655712,221297329,278047211,234,SRX5577630,SRS4539495,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.46793,,0.34168,,0.80734,,0.5874,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51380,SRR8787578,SRX5577629,SRS4539495,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 hnrnpa0a B1,iCLIP   iC hnrnpa0a B1 AGN001182,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001182|replicate order:1|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B1,AGR001627,AGR001627,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001627_R1.fastq.gz,fastq,626649019.0,21785135.0,AGR001627 R1.fastq.gz,0:28.76 1:0,A:180978164;C:117664846;G:144093534;T:183906538;N:5937,28,0,,,180978164,117664846,144093534,183906538,5937,SRX5577629,SRS4539495,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.47116,,0.3442,,0.80655,,0.58888,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51381,SRR8787579,SRX5577628,SRS4539494,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 srsf4 B1,iCLIP   iC srsf4 B1 AGN001181,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001025|replicate ref:AGN001181|replicate order:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP srsf4 B1,AGR001626,AGR001626,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001626_R1.fastq.gz,fastq,26882055.0,1016708.0,AGR001626 R1.fastq.gz,0:26.44 1:0,A:7601629;C:6720961;G:6312349;T:6247110;N:6,26,0,,,7601629,6720961,6312349,6247110,6,SRX5577628,SRS4539494,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.12624,,0.05031,,0.92099,,0.62874,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51382,SRR8787580,SRX5577627,SRS4539494,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 srsf4 B1,iCLIP   iC srsf4 B1 AGN001181,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001025|replicate ref:AGN001181|replicate order:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP srsf4 B1,AGR001625,AGR001625,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001625_R1.fastq.gz,fastq,19022228.0,719302.0,AGR001625 R1.fastq.gz,0:26.45 1:0,A:5340294;C:4692571;G:4510708;T:4478517;N:138,26,0,,,5340294,4692571,4510708,4478517,138,SRX5577627,SRS4539494,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.12739,,0.05334,,0.9205,,0.61225,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51383,SRR8787581,SRX5577626,SRS4539493,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 hnrnpa0a B3,iCLIP   iC hnrnpa0a B3 AGN001313,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001313|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B3,AGR001631,AGR001631,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001631_R1.fastq.gz,fastq,435541691.0,14051366.0,AGR001631 R1.fastq.gz,0:31.00 1:0,A:105298647;C:96108748;G:121537884;T:112592275;N:4137,31,0,,,105298647,96108748,121537884,112592275,4137,SRX5577626,SRS4539493,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.29884,,0.17976,,0.87375,,0.55383,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51384,SRR8787582,SRX5577625,SRS4539493,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 hnrnpa0a B3,iCLIP   iC hnrnpa0a B3 AGN001313,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001313|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B3,AGR001632,AGR001632,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001632_R1.fastq.gz,fastq,1060447048.0,34132191.0,AGR001632 R1.fastq.gz,0:31.07 1:0,A:257105081;C:233141636;G:294479896;T:275674763;N:45672,31,0,,,257105081,233141636,294479896,275674763,45672,SRX5577625,SRS4539493,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.30432,,0.18534,,0.87251,,0.52719,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51385,SRR8787583,SRX5577624,SRS4539492,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 hnrnpa0a B2,iCLIP   iC hnrnpa0a B2 AGN001312,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001312|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B2,AGR001630,AGR001630,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001630_R1.fastq.gz,fastq,2555423901.0,80936768.0,AGR001630 R1.fastq.gz,0:31.57 1:0,A:580749928;C:601107101;G:763488952;T:609969537;N:108383,31,0,,,580749928,601107101,763488952,609969537,108383,SRX5577624,SRS4539492,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.29202,,0.15612,,0.87129,,0.61251,,44,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures