rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
8055,ERR022484,ERX008924,ERS017427,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 2cells,SAMEA898400,Wellcome Sanger Institute,Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2cells,RNA from Zebrafish embryo 2cells,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_5.srf,srf,3947547008.0,25970704.0,E MTAB 434:4946 5.srf,0:76 1:76,A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500,76,76,,,1069302461,914233601,902631356,1055986090,5393500,ERX008924,ERS017427,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.93356,0.93346,0.03988,0.04022,0.79135,0.79198,0.48864,0.48464,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
8056,ERR022486,ERX008922,ERS012705,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 1 dpf,RNA from Zebrafish embryo 1 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_3.srf,srf,4788693120.0,31504560.0,E MTAB 434:5141 3.srf,0:76 1:76,A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244,76,76,,,1329328273,1071568772,1063807333,1316891498,7097244,ERX008922,ERS012705,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95867,0.95691,0.14543,0.14805,0.69753,0.70078,0.46273,0.47662,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
8057,ERR022488,ERX008921,ERS012706,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 3 dpf 2,SAMEA898404,Wellcome Sanger Institute,Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 3 dpf,RNA from Zebrafish embryo 3 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_6.srf,srf,3787933176.0,24920613.0,E MTAB 434:5141 6.srf,0:76 1:76,A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818,76,76,,,1051092006,842721213,838644314,1048667825,6807818,ERX008921,ERS012706,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95952,0.95914,0.16277,0.16553,0.66352,0.6661,0.46603,0.46879,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
8058,ERR022485,ERX008920,ERS017423,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 6hpf,SAMEA898399,Wellcome Sanger Institute,Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 6hpf,RNA from Zebrafish embryo 6hpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_6.srf,srf,5910514528.0,38884964.0,E MTAB 434:4946 6.srf,0:76 1:76,A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807,76,76,,,1741038828,1243493514,1214904056,1703863323,7214807,ERX008920,ERS017423,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.91619,0.91684,0.14961,0.15221,0.77189,0.7723,0.49092,0.49303,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Gastrula,Embryo,Whole Organism,All anatomical structures
8061,ERR022482,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_7.srf,srf,1764668160.0,16339520.0,E MTAB 434:2719 7.srf,0:54 1:54,A:470580161;C:399075336;G:417290042;T:474450367;N:3272254,54,54,,,470580161,399075336,417290042,474450367,3272254,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.9454,0.94288,0.20211,0.2029,0.66856,0.67207,0.4856,0.48119,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8062,ERR022483,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_8.srf,srf,1678321188.0,15540011.0,E MTAB 434:2719 8.srf,0:54 1:54,A:446988405;C:380486018;G:396533911;T:451117596;N:3195258,54,54,,,446988405,380486018,396533911,451117596,3195258,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94565,0.94277,0.19929,0.19877,0.66584,0.67014,0.47973,0.46826,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8063,ERR022487,ERX008918,ERS012707,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 2 dpf 2,SAMEA898403,Wellcome Sanger Institute,Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2 dpf,RNA from Zebrafish embryo 2 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:2 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_5.srf,srf,4321796696.0,28432873.0,E MTAB 434:5141 5.srf,0:76 1:76,A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424,76,76,,,1185782721,976784015,973264244,1178952292,7013424,ERX008918,ERS012707,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96001,0.95851,0.15373,0.15636,0.69051,0.69576,0.47409,0.47525,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Hatching,Embryo,Whole Organism,All anatomical structures
36405,SRR546820,SRX180750,SRS347212,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo prim6 stage,D. rerio prim6 embryo,D. rerio prim6 embryo,,,,,,,,,,,RNAseq   D. rerio prim6 embryo,RNAseq   D. rerio prim6 embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_prim6_2_fix.fastq,fastq,3011340704.0,19811452.0,RNAseq   D. rerio prim6 embryo,0:76 1:76,A:727345664;C:767747833;G:787766862;T:725606403;N:2873942,76,76,,,727345664,767747833,787766862,725606403,2873942,SRX180750,SRS347212,SRA055273,University of Bergen,ZEPROME consortium,2,0.94491,0.94492,0.04196,0.04323,0.76641,0.76928,0.48087,0.48787,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36406,SRR546819,SRX180749,SRS347211,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 14 somites stage,D. rerio 14 somites embryo,D. rerio 14 somites embryo,,,,,,,,,,,RNAseq   D. rerio 14 somites embryo,RNAseq   D. rerio 14 somites embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_14somites_2.fastq,fastq,2976465520.0,19582010.0,RNAseq   D. rerio 14 somites embryo,0:76 1:76,A:747831748;C:733533938;G:754151936;T:738091995;N:2855903,76,76,,,747831748,733533938,754151936,738091995,2855903,SRX180749,SRS347211,SRA055273,University of Bergen,ZEPROME consortium,2,0.9236,0.91427,0.0861,0.08534,0.7559,0.75528,0.48428,0.47549,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
36407,SRR546818,SRX180748,SRS347209,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage,D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,,,,,,,,,,,RNAseq   D. rerio dome/zfs:0000015 embryo,RNAseq   D. rerio dome/zfs:0000015 embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_30p_dome_1.fastq,fastq,2359648608.0,15524004.0,RNAseq   D. rerio dome/zfs:0000015 embryo,0:76 1:76,A:588562906;C:575605218;G:603310130;T:589755481;N:2414873,76,76,,,588562906,575605218,603310130,589755481,2414873,SRX180748,SRS347209,SRA055273,University of Bergen,ZEPROME consortium,2,0.89779,0.9222,0.04122,0.0431,0.76609,0.77112,0.49779,0.49305,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36408,SRR546817,SRX180747,SRS358988,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 2 cells stage,D. rerio 2 cells embryo,D. rerio 2 cells embryo,,,,,,,,,,,RNAseq   D. rerio 2 cells embryo,RNAseq   D. rerio 2 cells embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,2799828144.0,18419922.0,RNAseq   D. rerio 2 cells embryo,0:76 1:76,A:678251421;C:711410510;G:729905459;T:677312772;N:2947982,76,76,,,678251421,711410510,729905459,677312772,2947982,SRX180747,SRS358988,SRA055273,University of Bergen,ZEPROME consortium,2,0.9498,0.94704,0.02363,0.02442,0.7988,0.80221,0.48657,0.49361,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
39751,SRR2422954,SRX1092140,SRS987764,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFAB KD,U2AFA2B KD,U2A2FA and U2AF2B knockdown,,treatment:U2AF2A B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2A and U2AF2B KD,U2AFAB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz,fastq fastq,4010033906.0,19851653.0,u2afa u2afb kd,0:101 1:101,A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449,101,101,,,954988404,1049486839,1028325376,975960838,1272449,SRX1092140,SRS987764,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88891,0.88704,0.22441,0.2245,0.73781,0.74111,0.60755,0.61314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39752,SRR2422968,SRX1092139,SRS987762,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFB KD,U2AF2B KD,U2AF2B knockdown,,treatment:U2AF2B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2B KD,U2AFB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz,fastq fastq,3657236866.0,18105133.0,u2af2b kd,0:101 1:101,A:859906359;C:963846892;G:950183263;T:882292781;N:1007571,101,101,,,859906359,963846892,950183263,882292781,1007571,SRX1092139,SRS987762,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.87685,0.87325,0.21282,0.21347,0.74899,0.75166,0.65013,0.65163,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39753,SRR2422941,SRX1092136,SRS987760,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,Control1,Control1,Control1,,treatment:Control 1|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 1,Control1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz,fastq fastq,5446154724.0,26961162.0,control1,0:101 1:101,A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287,101,101,,,1236792250,1484635192,1463483173,1259686822,1557287,SRX1092136,SRS987760,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88645,0.88416,0.23061,0.23167,0.75872,0.75921,0.63459,0.63891,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39754,SRR2422967,SRX1092138,SRS987763,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFA KD,U2AF2A KD,U2AF2A knockdown,,treatment:U2AF2A morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF A KD,U2AFA KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz,fastq fastq,7385905174.0,36563887.0,u2af2a kd,0:101 1:101,A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609,101,101,,,1742999157,1956220866,1920103000,1764198542,2383609,SRX1092138,SRS987763,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.74404,0.74051,0.14971,0.14762,0.76641,0.76757,0.56197,0.56515,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39755,SRR2422942,SRX1092137,SRS987761,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,Control2,Control2,Control2,,treatment:Control 2|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 2,Control 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz,fastq fastq,4226478926.0,20923163.0,control2,0:101 1:101,A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890,101,101,,,1005765442,1098720686,1084955814,1035764094,1272890,SRX1092137,SRS987761,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.83225,0.83092,0.22325,0.22374,0.75396,0.75603,0.6203,0.61868,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39934,SRR2473238,SRX1270438,SRS1078341,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio embryos ectopically expressing human SPOPwt.,,Danio rerio ectopic SPOPwt,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOPwt,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz,fastq fastq,6185345892.0,60640646.0,Danio rerio ectopic SPOPwt,0:51 1:51,A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809,51,51,,,1647678166,1462773970,1416249443,1657464504,1179809,SRX1270438,SRS1078341,,,Weill Cornell Medical College,2,0.94598,0.94553,0.09216,0.0934,0.68789,0.69065,0.46814,0.47172,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
39935,SRR2473236,SRX1270437,SRS1078340,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio ectopically expressing SPOP F133V,,Danio rerio ectopic SPOP F133V,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOP F133V,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz,fastq fastq,6130528134.0,60103217.0,Danio rerio ectopic SPOP F133V,0:51 1:51,A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035,51,51,,,1630145057,1450811256,1409924927,1638457859,1189035,SRX1270437,SRS1078340,,,Weill Cornell Medical College,2,0.9444,0.94139,0.09809,0.0979,0.68487,0.68657,0.46751,0.47276,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
39936,SRR2473235,SRX1270436,SRS1078339,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,,,Danio rerio SPOP morpholino,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio SPOP morpholino,Danio rerio SPOP morpholino,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz,fastq fastq,5693947938.0,55823019.0,Danio rerio SPOP morpholino,0:51 1:51,A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641,51,51,,,1513477521,1350461483,1305374194,1523527099,1107641,SRX1270436,SRS1078339,,,Weill Cornell Medical College,2,0.94534,0.94431,0.09368,0.0945,0.68941,0.69077,0.46543,0.46749,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
40711,SRR3420419,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz,fastq fastq,2419781176.0,15919613.0,AG00719 run 1,0:76 1:76,A:738997601;C:465047900;G:477140497;T:733241052;N:5354126,76,76,,,738997601,465047900,477140497,733241052,5354126,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.78184,0.71182,0.66469,0.60037,0.75743,0.77518,0.53432,0.52801,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40712,SRR3420420,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz,fastq fastq,3074724552.0,20228451.0,AG00719 run 2,0:76 1:76,A:918671897;C:609510609;G:622542852;T:922439528;N:1559666,76,76,,,918671897,609510609,622542852,922439528,1559666,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76444,0.65488,0.65157,0.55185,0.75741,0.78106,0.53067,0.52622,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40713,SRR3420421,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz,fastq fastq,2666395856.0,17542078.0,AG00719 run 3,0:76 1:76,A:787508876;C:539791618;G:549145516;T:785088342;N:4861504,76,76,,,787508876,539791618,549145516,785088342,4861504,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.75479,0.69465,0.63843,0.58422,0.75716,0.78423,0.53952,0.52615,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40714,SRR3420388,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz,fastq fastq,2699903800.0,17762525.0,AG00718 run 1,0:76 1:76,A:832300161;C:503956886;G:525141498;T:832566681;N:5938574,76,76,,,832300161,503956886,525141498,832566681,5938574,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76651,0.69033,0.63937,0.56749,0.77145,0.78545,0.53429,0.53165,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40715,SRR3420392,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz,fastq fastq,2798947456.0,18414128.0,AG00718 run 2,0:76 1:76,A:853546590;C:536347349;G:556751964;T:851863324;N:438229,76,76,,,853546590,536347349,556751964,851863324,438229,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74665,0.63683,0.6265,0.5237,0.76134,0.7905,0.54613,0.53982,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40716,SRR3420398,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz,fastq fastq,1442918520.0,9492885.0,AG00717 run 1,0:76 1:76,A:442675510;C:273265985;G:284514997;T:439403136;N:3058892,76,76,,,442675510,273265985,284514997,439403136,3058892,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76736,0.69048,0.60693,0.53532,0.74647,0.76138,0.51546,0.5135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40717,SRR3420402,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz,fastq fastq,2524099688.0,16605919.0,AG00717 run 2,0:76 1:76,A:752163917;C:500880325;G:526291920;T:744462824;N:300702,76,76,,,752163917,500880325,526291920,744462824,300702,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.7274,0.651,0.57791,0.50498,0.74434,0.76329,0.51831,0.50479,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40718,SRR3420405,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz,fastq fastq,1320586032.0,8688066.0,AG00717 run 3,0:76 1:76,A:394339370;C:259687848;G:270914284;T:389960707;N:5683823,76,76,,,394339370,259687848,270914284,389960707,5683823,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72219,0.6734,0.55665,0.5122,0.75371,0.76323,0.5098,0.50658,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40719,SRR3420409,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz,fastq fastq,1778143272.0,11698311.0,AG00717 run 4,0:76 1:76,A:531893644;C:351009327;G:366187476;T:528937189;N:115636,76,76,,,531893644,351009327,366187476,528937189,115636,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72027,0.6573,0.57252,0.50814,0.74913,0.77479,0.51537,0.50066,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40720,SRR3420315,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz,fastq fastq,1837024424.0,12085687.0,AG00716 run 1,0:76 1:76,A:571581150;C:339887376;G:357200726;T:564453542;N:3901630,76,76,,,571581150,339887376,357200726,564453542,3901630,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.77818,0.69777,0.64211,0.56481,0.75503,0.76926,0.50584,0.51507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40721,SRR3420319,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz,fastq fastq,2763994600.0,18184175.0,AG00716 run 2,0:76 1:76,A:841712204;C:530711238;G:562110067;T:828853061;N:608030,76,76,,,841712204,530711238,562110067,828853061,608030,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74716,0.66787,0.61425,0.53764,0.7475,0.76518,0.50855,0.51311,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40722,SRR3420323,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz,fastq fastq,1055704904.0,6945427.0,AG00716 run 3,0:76 1:76,A:323142351;C:199674907;G:210508599;T:317806564;N:4572483,76,76,,,323142351,199674907,210508599,317806564,4572483,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.73664,0.68701,0.59387,0.5447,0.76179,0.76132,0.51299,0.51552,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40723,SRR3420327,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz,fastq fastq,2526928408.0,16624529.0,AG00716 run 4,0:76 1:76,A:771333886;C:482964782;G:508687112;T:763609426;N:333202,76,76,,,771333886,482964782,508687112,763609426,333202,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74535,0.66478,0.61452,0.53584,0.75826,0.77329,0.51139,0.51539,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
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
41381,SRR4375307,SRX2226800,SRS1732678,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B1,resa AG01072,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B1,AG01072.1,AG01072.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz,fastq fastq,756436968.0,4976559.0,AG01072.1 R2.fastq.gz,0:76 1:76,A:277813562;C:101592220;G:103435859;T:273576694;N:18633,76,76,,,277813562,101592220,103435859,273576694,18633,SRX2226800,SRS1732678,SRA482696,Yale University|Genetics,Yale University,2,0.00777,0.00795,0.00043,0.00056,0.99344,0.99389,0.43869,0.43095,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-10-06,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41382,SRR4375306,SRX2226799,SRS1732692,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B3,resa AG01070,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B3,AG01070.1,AG01070.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz,fastq fastq,601712368.0,3958634.0,AG01070.1 R2.fastq.gz,0:76 1:76,A:188474921;C:113643606;G:114382568;T:185195364;N:15909,76,76,,,188474921,113643606,114382568,185195364,15909,SRX2226799,SRS1732692,SRA482696,Yale University|Genetics,Yale University,2,0.84037,0.84016,0.03493,0.03544,0.97303,0.97252,0.46337,0.47093,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41383,SRR4375305,SRX2226798,SRS1732691,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B2,resa AG01069,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B2,AG01069.1,AG01069.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz,fastq fastq,1344477848.0,8845249.0,AG01069.1 R1.fastq.gz,0:76 1:76,A:418545593;C:256422789;G:257715519;T:411760293;N:33654,76,76,,,418545593,256422789,257715519,411760293,33654,SRX2226798,SRS1732691,SRA482696,Yale University|Genetics,Yale University,2,0.84542,0.84566,0.03642,0.03588,0.97084,0.97197,0.4739,0.48121,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41384,SRR4375304,SRX2226797,SRS1732690,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h pA r3 B1,resa AG01068,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h pA r3 B1,AG01068.1,AG01068.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz,fastq fastq,896200056.0,5896053.0,AG01068.1 R2.fastq.gz,0:76 1:76,A:278768309;C:171161843;G:172303088;T:273944252;N:22564,76,76,,,278768309,171161843,172303088,273944252,22564,SRX2226797,SRS1732690,SRA482696,Yale University|Genetics,Yale University,2,0.83862,0.83897,0.0351,0.03585,0.97183,0.97204,0.47364,0.47138,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41385,SRR4375303,SRX2226796,SRS1732689,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B3,resa AG01067,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B3,AG01067.1,AG01067.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz,fastq fastq,1799778192.0,11840646.0,AG01067.1 R1.fastq.gz,0:76 1:76,A:561491448;C:342221462;G:343998479;T:552022535;N:44268,76,76,,,561491448,342221462,343998479,552022535,44268,SRX2226796,SRS1732689,SRA482696,Yale University|Genetics,Yale University,2,0.84432,0.84397,0.03554,0.03522,0.97224,0.9725,0.46732,0.46922,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41386,SRR4375302,SRX2226795,SRS1732688,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B2,resa AG01066,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B2,AG01066.1,AG01066.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz,fastq fastq,1313436864.0,8641032.0,AG01066.1 R2.fastq.gz,0:76 1:76,A:409666264;C:249755645;G:251028600;T:402953610;N:32745,76,76,,,409666264,249755645,251028600,402953610,32745,SRX2226795,SRS1732688,SRA482696,Yale University|Genetics,Yale University,2,0.84584,0.84611,0.0349,0.03543,0.97189,0.97175,0.47547,0.48555,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41387,SRR4375301,SRX2226794,SRS1732687,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 8h L430 pA r3 B1,resa AG01065,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 8h L430 pA r3 B1,AG01065.1,AG01065.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz,fastq fastq,1442385152.0,9489376.0,AG01065.1 R2.fastq.gz,0:76 1:76,A:449362282;C:274879749;G:276626223;T:441480173;N:36725,76,76,,,449362282,274879749,276626223,441480173,36725,SRX2226794,SRS1732687,SRA482696,Yale University|Genetics,Yale University,2,0.8417,0.84205,0.03519,0.03559,0.97193,0.97179,0.47697,0.46118,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41388,SRR4375300,SRX2226793,SRS1732685,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA CLIP Ago2   RESA CLIP Ago2 input,resa clip ago2 AG01631,,strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:5% input before pulldown|condition:input|BioSampleModel:Model organism or animal,,,,,,,,,RESA CLIP Ago2   RESA CLIP Ago2 input,AG01631.1,AG01631.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz,fastq fastq,9864834960.0,64900230.0,AG01631.1 R2.fastq.gz,0:76 1:76,A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520,76,76,,,2990534603,1958949912,1963153108,2951932817,264520,SRX2226793,SRS1732685,SRA482696,Yale University|Genetics,Yale University,2,0.83121,0.85078,0.03505,0.0364,0.97171,0.97019,0.46925,0.47246,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
41389,SRR4375299,SRX2226779,SRS1732684,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA CLIP Ago2   RESA CLIP Ago2 IP,resa clip ago2 AG01630,,strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:flag bead pulldown post crosslinking|condition:Ago2 IP|BioSampleModel:Model organism or animal,,,,,,,,,RESA CLIP Ago2   RESA CLIP Ago2 IP,AG01630.1,AG01630.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz,fastq fastq,9348207632.0,61501366.0,AG01630.1 R1.fastq.gz,0:76 1:76,A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848,76,76,,,2819572908,1871537719,1881735941,2775115216,245848,SRX2226779,SRS1732684,SRA482696,Yale University|Genetics,Yale University,2,0.80207,0.78648,0.02992,0.02839,0.97885,0.97871,0.49297,0.49107,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
41390,SRR4375197,SRX2226727,SRS1732683,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B3,resa AG01086,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B3,AG01086.2,AG01086.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz,fastq fastq,714848400.0,4702950.0,AG01086.2 R2.fastq.gz,0:76 1:76,A:261928616;C:96586565;G:97768464;T:258351392;N:213363,76,76,,,261928616,96586565,97768464,258351392,213363,SRX2226727,SRS1732683,SRA482696,Yale University|Genetics,Yale University,2,0.00715,0.00733,0.00046,0.00044,0.99417,0.99435,0.46775,0.42207,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41391,SRR4375176,SRX2226710,SRS1732686,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 64c pA r3 B2,resa AG01061,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 64c pA r3 B2,AG01061.1,AG01061.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz,fastq fastq,724448416.0,4766108.0,AG01061.1 R2.fastq.gz,0:76 1:76,A:224701149;C:138989041;G:139762199;T:220977796;N:18231,76,76,,,224701149,138989041,139762199,220977796,18231,SRX2226710,SRS1732686,SRA482696,Yale University|Genetics,Yale University,2,0.84913,0.84756,0.03557,0.03568,0.97153,0.97116,0.47281,0.46157,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-10-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41392,SRR4375175,SRX2226709,SRS1732683,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B3,resa AG01086,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B3,AG01086.1,AG01086.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz,fastq fastq,411922128.0,2710014.0,AG01086.1 R1.fastq.gz,0:76 1:76,A:150812258;C:55795177;G:56809368;T:148495332;N:9993,76,76,,,150812258,55795177,56809368,148495332,9993,SRX2226709,SRS1732683,SRA482696,Yale University|Genetics,Yale University,2,0.00798,0.00746,0.00062,0.00055,0.99385,0.99399,0.44328,0.47308,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41393,SRR4375146,SRX2226694,SRS1732682,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B2,resa AG01085,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B2,AG01085.2,AG01085.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz,fastq fastq,700337720.0,4607485.0,AG01085.2 R1.fastq.gz,0:76 1:76,A:256568404;C:94627005;G:95783677;T:253149693;N:208941,76,76,,,256568404,94627005,95783677,253149693,208941,SRX2226694,SRS1732682,SRA482696,Yale University|Genetics,Yale University,2,0.00733,0.00726,0.00055,0.00048,0.99413,0.99393,0.46893,0.45795,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41394,SRR4375102,SRX2226674,SRS1732682,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B2,resa AG01085,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B2,AG01085.1,AG01085.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz,fastq fastq,409587712.0,2694656.0,AG01085.1 R1.fastq.gz,0:76 1:76,A:149931448;C:55481183;G:56493706;T:147671446;N:9929,76,76,,,149931448,55481183,56493706,147671446,9929,SRX2226674,SRS1732682,SRA482696,Yale University|Genetics,Yale University,2,0.0079,0.0078,0.00056,0.0005,0.99366,0.99385,0.42647,0.47214,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41395,SRR4375101,SRX2226673,SRS1732681,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B1,resa AG01084,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B1,AG01084.2,AG01084.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz,fastq fastq,396825488.0,2610694.0,AG01084.2 R1.fastq.gz,0:76 1:76,A:145317384;C:53679748;G:54375412;T:143331621;N:121323,76,76,,,145317384,53679748,54375412,143331621,121323,SRX2226673,SRS1732681,SRA482696,Yale University|Genetics,Yale University,2,0.0071,0.00673,0.00044,0.00042,0.99417,0.99419,0.44659,0.45357,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41396,SRR4375100,SRX2226672,SRS1732681,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 8h B1,resa AG01084,,strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 8h B1,AG01084.1,AG01084.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz,fastq fastq,236514888.0,1556019.0,AG01084.1 R1.fastq.gz,0:76 1:76,A:86560104;C:32062698;G:32664624;T:85221432;N:6030,76,76,,,86560104,32062698,32664624,85221432,6030,SRX2226672,SRS1732681,SRA482696,Yale University|Genetics,Yale University,2,0.00756,0.00706,0.00061,0.00064,0.99405,0.99419,0.47228,0.48736,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
41397,SRR4375099,SRX2226671,SRS1732680,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B3,resa AG01074,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B3,AG01074.2,AG01074.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz,fastq fastq,1411678568.0,9287359.0,AG01074.2 R1.fastq.gz,0:76 1:76,A:518452828;C:189515599;G:191777773;T:511511925;N:420443,76,76,,,518452828,189515599,191777773,511511925,420443,SRX2226671,SRS1732680,SRA482696,Yale University|Genetics,Yale University,2,0.00745,0.00729,0.00047,0.00045,0.99405,0.99411,0.43814,0.47981,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41398,SRR4375098,SRX2226670,SRS1732680,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B3,resa AG01074,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B3,AG01074.1,AG01074.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01074.1_R1.fastq.gz AG01074.1_R2.fastq.gz,fastq fastq,867077312.0,5704456.0,AG01074.1 R1.fastq.gz,0:76 1:76,A:318238609;C:116633576;G:118737324;T:313446459;N:21344,76,76,,,318238609,116633576,118737324,313446459,21344,SRX2226670,SRS1732680,SRA482696,Yale University|Genetics,Yale University,2,0.00791,0.00753,0.00052,0.00054,0.99395,0.99381,0.45038,0.44477,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41399,SRR4375097,SRX2226669,SRS1732679,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B2,resa AG01073,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B2,AG01073.2,AG01073.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01073.2_R1.fastq.gz AG01073.2_R2.fastq.gz,fastq fastq,1170921968.0,7703434.0,AG01073.2 R1.fastq.gz,0:76 1:76,A:430252673;C:156958676;G:158824982;T:424542052;N:343585,76,76,,,430252673,156958676,158824982,424542052,343585,SRX2226669,SRS1732679,SRA482696,Yale University|Genetics,Yale University,2,0.00759,0.00753,0.00044,0.00046,0.99389,0.99375,0.48023,0.49305,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41400,SRR4375096,SRX2226668,SRS1732679,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B2,resa AG01073,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B2,AG01073.1,AG01073.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01073.1_R1.fastq.gz AG01073.1_R2.fastq.gz,fastq fastq,650729936.0,4281118.0,AG01073.1 R1.fastq.gz,0:76 1:76,A:238957997;C:87418913;G:88996057;T:235340339;N:16630,76,76,,,238957997,87418913,88996057,235340339,16630,SRX2226668,SRS1732679,SRA482696,Yale University|Genetics,Yale University,2,0.00771,0.00754,0.00052,0.00049,0.99403,0.9936,0.46484,0.42136,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41401,SRR4375095,SRX2226667,SRS1732678,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Mut 64c B1,resa AG01072,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Mut 64c B1,AG01072.2,AG01072.2,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01072.2_R1.fastq.gz AG01072.2_R2.fastq.gz,fastq fastq,1293717904.0,8511302.0,AG01072.2 R1.fastq.gz,0:76 1:76,A:475476006;C:173352933;G:175448573;T:469059516;N:380876,76,76,,,475476006,173352933,175448573,469059516,380876,SRX2226667,SRS1732678,SRA482696,Yale University|Genetics,Yale University,2,0.0072,0.0071,0.00042,0.00038,0.99397,0.99385,0.4403,0.43351,76,76,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
41402,SRR4375094,SRX2226666,SRS1732677,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   WT 64c pA r3 B1,resa AG01060,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   WT 64c pA r3 B1,AG01060.1,AG01060.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG01060.1_R1.fastq.gz AG01060.1_R2.fastq.gz,fastq fastq,531097120.0,3494060.0,AG01060.1 R1.fastq.gz,0:76 1:76,A:164891814;C:101739900;G:102440303;T:162011179;N:13924,76,76,,,164891814,101739900,102440303,162011179,13924,SRX2226666,SRS1732677,SRA482696,Yale University|Genetics,Yale University,2,0.84523,0.84587,0.03561,0.03503,0.9723,0.97161,0.46204,0.47901,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41403,SRR4375093,SRX2226665,SRS1732676,SRP090954,PRJNA345638,RESA identifies mRNA regulatory sequences with high resolution,PRJNA345638,Other,Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.,,,,RESA Seq   Needle r2,resa AG00580,,strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|condition:needle|BioSampleModel:Model organism or animal,,,,,,,,,RESA Seq   Needle r2,AG00580.1,AG00580.1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP090954,,,AG00580.1_R1.fastq.gz AG00580.1_R2.fastq.gz,fastq fastq,536691936.0,3530868.0,AG00580.1 R1.fastq.gz,0:76 1:76,A:162711942;C:106417027;G:106484569;T:160130705;N:947693,76,76,,,162711942,106417027,106484569,160130705,947693,SRX2226665,SRS1732676,SRA482696,Yale University|Genetics,Yale University,2,0.85835,0.85877,0.03686,0.03615,0.96818,0.96895,0.47111,0.47948,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-12-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
42492,SRR5681431,SRX2916758,SRS2282896,SRP109143,PRJNA389374,Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis,PRJNA389374,Whole Genome Sequencing,the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.,,,,,15um,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:15um|BioSampleModel:Model organism or animal,,,,,,,,,15um zebrafish,15um zebrafish,15um zebrafish,15um zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP109143,,,15um_2.fq.gz 15um_1.fq.gz,fastq fastq,4510379400.0,22551897.0,15um 2.fq.gz,0:100 1:100,A:1183709237;C:1078933188;G:1057042534;T:1190615427;N:79014,100,100,,,1183709237,1078933188,1057042534,1190615427,79014,SRX2916758,SRS2282896,SRA574072,The Chinese University of HongKong|School of Biomedical Sciences,The Chinese University of HongKong,2,0.95073,0.95055,0.0647,0.06526,0.67176,0.67351,0.46247,0.46176,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,China,2017-06-14,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
42493,SRR5681432,SRX2916757,SRS2282895,SRP109143,PRJNA389374,Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis,PRJNA389374,Whole Genome Sequencing,the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.,,,,,10um,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:10um|BioSampleModel:Model organism or animal,,,,,,,,,10um zebrafish,10um zebrafish,10um zebrafish,10um zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP109143,,,10um_1.fq.gz 10um_2.fq.gz,fastq fastq,4513300800.0,22566504.0,10um 1.fq.gz,0:100 1:100,A:1186008993;C:1078123999;G:1056044415;T:1193043558;N:79835,100,100,,,1186008993,1078123999,1056044415,1193043558,79835,SRX2916757,SRS2282895,SRA574072,The Chinese University of HongKong|School of Biomedical Sciences,The Chinese University of HongKong,2,0.94799,0.94687,0.07002,0.06979,0.66667,0.66746,0.47255,0.47338,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,China,2017-06-14,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
42494,SRR5681433,SRX2916756,SRS2282894,SRP109143,PRJNA389374,Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis,PRJNA389374,Whole Genome Sequencing,the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.,,,,,control,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,control zebrafish,control zebrafish,control zebrafish,control zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP109143,,,con_1.fq.gz con_2.fq.gz,fastq fastq,4514603400.0,22573017.0,con 2.fq.gz,0:100 1:100,A:1183878943;C:1081336890;G:1058805201;T:1190503424;N:78942,100,100,,,1183878943,1081336890,1058805201,1190503424,78942,SRX2916756,SRS2282894,SRA574072,The Chinese University of HongKong|School of Biomedical Sciences,The Chinese University of HongKong,2,0.951,0.95009,0.0669,0.06735,0.6659,0.66681,0.46599,0.46703,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,China,2017-06-14,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
46211,SRR6477199,SRX3567065,SRS2838997,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq Bud13   Bud13 Sibling 30h,RNAseq Bud13   Bud13 Sib 30h AG01145,,strain:TU/AB|age:30.0|dev stage:30h|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:2|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Bud13   Bud13 Sibling 30h,AG01145.2,AG01145.2,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP129892,,,AG01145.2_R2.fastq.gz AG01145.2_R1.fastq.gz,fastq fastq,12323940056.0,81078553.0,AG01145.2 R1.fastq.gz,0:76 1:76,A:3425803431;C:2777524766;G:2722925333;T:3380952969;N:16733557,76,76,,,3425803431,2777524766,2722925333,3380952969,16733557,SRX3567065,SRS2838997,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94345,0.94709,0.12521,0.12335,0.69165,0.69475,0.4685,0.47082,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-01-17,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
46212,SRR6477200,SRX3567064,SRS2838996,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq Bud13   Bud13 KO 30h,RNAseq Bud13   Bud13 KO 30h AG01144,,strain:TU/AB|age:30.0|dev stage:30h|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Bud13   Bud13 KO 30h,AG01144.2,AG01144.2,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP129892,,,AG01144.2_R1.fastq.gz AG01144.2_R2.fastq.gz,fastq fastq,12242377920.0,80541960.0,AG01144.2 R1.fastq.gz,0:76 1:76,A:3501235324;C:2524126832;G:2520934401;T:3679154562;N:16926801,76,76,,,3501235324,2524126832,2520934401,3679154562,16926801,SRX3567064,SRS2838996,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93874,0.93814,0.2229,0.17671,0.71102,0.71234,0.48631,0.48352,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
46213,SRR6477201,SRX3567063,SRS2838995,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq RES complex   rbmx2 SIB 48h,RNAseq RES complex   rbmx2 SIB 48h AG01558,,strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:4|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq RES complex   rbmx2 SIB 48h,AG01558.1,AG01558.1,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP129892,,,AG01558.1_R1.fastq.gz AG01558.1_R2.fastq.gz,fastq fastq,9241524912.0,60799506.0,AG01558.1 R2.fastq.gz,0:76 1:76,A:2590261461;C:2051008707;G:2048932825;T:2547072369;N:4249550,76,76,,,2590261461,2051008707,2048932825,2547072369,4249550,SRX3567063,SRS2838995,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94691,0.94614,0.14206,0.14368,0.68093,0.68004,0.46358,0.46633,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
46214,SRR6477202,SRX3567062,SRS2838994,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq RES complex   rbmx2 KO 48h,RNAseq RES complex   rbmx2 KO 48h AG01557,,strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:3|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq RES complex   rbmx2 KO 48h,AG01557.1,AG01557.1,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP129892,,,AG01557.1_R1.fastq.gz AG01557.1_R2.fastq.gz,fastq fastq,10308923480.0,67821865.0,AG01557.1 R2.fastq.gz,0:76 1:76,A:2867250947;C:2265018715;G:2268705348;T:2903182748;N:4765722,76,76,,,2867250947,2265018715,2268705348,2903182748,4765722,SRX3567062,SRS2838994,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93752,0.94003,0.18012,0.18634,0.68893,0.6858,0.46131,0.46347,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
46215,SRR6477203,SRX3567061,SRS2838993,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq RES complex   snip1 SIB 48h,RNAseq RES complex   snip1 SIB 48h AG01560,,strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:6|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq RES complex   snip1 SIB 48h,AG01560.1,AG01560.1,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP129892,,,AG01560.1_R1.fastq.gz AG01560.1_R2.fastq.gz,fastq fastq,12336748336.0,81162818.0,AG01560.1 R2.fastq.gz,0:76 1:76,A:3381905039;C:2782580059;G:2774648248;T:3391983732;N:5631258,76,76,,,3381905039,2782580059,2774648248,3391983732,5631258,SRX3567061,SRS2838993,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94802,0.9492,0.13035,0.13145,0.68006,0.67783,0.46768,0.46426,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
46216,SRR6477204,SRX3567060,SRS2838992,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq RES complex   snip1 KO 48h,RNAseq RES complex   snip1 KO 48h AG01559,,strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:5|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq RES complex   snip1 KO 48h,AG01559.1,AG01559.1,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP129892,,,AG01559.1_R1.fastq.gz AG01559.1_R2.fastq.gz,fastq fastq,11252234568.0,74027859.0,AG01559.1 R1.fastq.gz,0:76 1:76,A:3167425566;C:2465030272;G:2448402147;T:3166105639;N:5270944,76,76,,,3167425566,2465030272,2448402147,3166105639,5270944,SRX3567060,SRS2838992,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93557,0.9354,0.19378,0.19524,0.69075,0.6943,0.46751,0.47134,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
48356,SRR5893042,SRX3058803,SRS2404515,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 64c R0 B2,dev timecourse AG00671,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 64c R0 B2,AG00671.2,AG00671.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00671.2_R1.fastq.gz AG00671.2_R2.fastq.gz,fastq fastq,3401007752.0,22375051.0,AG00671.2 R1.fastq.gz,0:76 1:76,A:761237295;C:934945811;G:938845233;T:765218661;N:760752,76,76,,,761237295,934945811,938845233,765218661,760752,SRX3058803,SRS2404515,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.71455,0.77271,0.06416,0.06853,0.77017,0.77189,0.48808,0.48936,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,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
48358,SRR5893044,SRX3058801,SRS2404514,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 64c pA B1,dev timecourse AG00644,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 64c pA B1,AG00644.1,AG00644.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00644.1_R1.fastq.gz AG00644.1_R2.fastq.gz,fastq fastq,2457941384.0,16170667.0,AG00644.1 R2.fastq.gz,0:76 1:76,A:655179090;C:570607586;G:571155579;T:658430586;N:2568543,76,76,,,655179090,570607586,571155579,658430586,2568543,SRX3058801,SRS2404514,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94406,0.94075,0.02483,0.02699,0.76936,0.76966,0.48505,0.48646,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48359,SRR5893045,SRX3058800,SRS2404517,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 64c pA B2,dev timecourse AG00645,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:1|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 64c pA B2,AG00645.1,AG00645.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00645.1_R1.fastq.gz AG00645.1_R2.fastq.gz,fastq fastq,2643787680.0,17393340.0,AG00645.1 R1.fastq.gz,0:76 1:76,A:704257377;C:614686679;G:614950025;T:707119985;N:2773614,76,76,,,704257377,614686679,614950025,707119985,2773614,SRX3058800,SRS2404517,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93726,0.94194,0.02686,0.02578,0.76834,0.76893,0.48339,0.47898,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,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
48362,SRR5893048,SRX3058797,SRS2404520,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield pA B1,dev timecourse AG00658,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:3|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield pA B1,AG00658.1,AG00658.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00658.1_R2.fastq.gz AG00658.1_R1.fastq.gz,fastq fastq,2368759640.0,15583945.0,AG00658.1 R2.fastq.gz,0:76 1:76,A:643327175;C:540895938;G:540699719;T:641357257;N:2479551,76,76,,,643327175,540895938,540699719,641357257,2479551,SRX3058797,SRS2404520,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.89596,0.89407,0.07479,0.07678,0.76004,0.7595,0.48733,0.48807,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48363,SRR5893049,SRX3058796,SRS2404521,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield pA B2,dev timecourse AG00659,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:3|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield pA B2,AG00659.1,AG00659.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00659.1_R1.fastq.gz AG00659.1_R2.fastq.gz,fastq fastq,2038811568.0,13413234.0,AG00659.1 R2.fastq.gz,0:76 1:76,A:558819941;C:458698081;G:460805877;T:558399462;N:2088207,76,76,,,558819941,458698081,460805877,558399462,2088207,SRX3058796,SRS2404521,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.92967,0.92885,0.0788,0.08121,0.75661,0.75631,0.49269,0.49182,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2017-08-03,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48364,SRR5893050,SRX3058795,SRS2404522,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 64c R0 B1,dev timecourse AG00670,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 64c R0 B1,AG00670.1,AG00670.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00670.1_R1.fastq.gz AG00670.1_R2.fastq.gz,fastq fastq,2692216248.0,17711949.0,AG00670.1 R1.fastq.gz,0:76 1:76,A:681268366;C:669533858;G:662344502;T:673374314;N:5695208,76,76,,,681268366,669533858,662344502,673374314,5695208,SRX3058795,SRS2404522,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.858,0.83961,0.06542,0.06545,0.76623,0.76463,0.47797,0.48023,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48365,SRR5893051,SRX3058794,SRS2404515,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 64c R0 B2,dev timecourse AG00671,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT 64c R0 B2,AG00671.1,AG00671.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00671.1_R1.fastq.gz AG00671.1_R2.fastq.gz,fastq fastq,1411014176.0,9282988.0,AG00671.1 R2.fastq.gz,0:76 1:76,A:356427462;C:351288483;G:348446516;T:351946038;N:2905677,76,76,,,356427462,351288483,348446516,351946038,2905677,SRX3058794,SRS2404515,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.83575,0.85161,0.06672,0.06526,0.76416,0.76615,0.48088,0.47816,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48366,SRR5893064,SRX3058781,SRS2404533,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 64c R0 B1,dev timecourse AG00728,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:10|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 64c R0 B1,AG00728.1,AG00728.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00728.1_R1.fastq.gz AG00728.1_R2.fastq.gz,fastq fastq,2789035232.0,18348916.0,AG00728.1 R1.fastq.gz,0:76 1:76,A:746104532;C:614735198;G:636481842;T:785596249;N:6117411,76,76,,,746104532,614735198,636481842,785596249,6117411,SRX3058781,SRS2404533,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.51926,0.49218,0.08229,0.0936,0.80744,0.8103,0.48989,0.48658,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48367,SRR5893065,SRX3058780,SRS2404535,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am shield pA B2,dev timecourse AG00701,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:9|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am shield pA B2,AG00701.1,AG00701.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00701.1_R1.fastq.gz AG00701.1_R2.fastq.gz,fastq fastq,2611389944.0,17180197.0,AG00701.1 R1.fastq.gz,0:76 1:76,A:696886025;C:607737206;G:605609129;T:699045963;N:2111621,76,76,,,696886025,607737206,605609129,699045963,2111621,SRX3058780,SRS2404535,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.9089,0.91353,0.03824,0.03668,0.78261,0.78293,0.49562,0.49348,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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
48369,SRR5893067,SRX3058778,SRS2404533,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 64c R0 B1,dev timecourse AG00728,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:10|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 64c R0 B1,AG00728.2,AG00728.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00728.2_R1.fastq.gz AG00728.2_R2.fastq.gz,fastq fastq,3094128568.0,20356109.0,AG00728.2 R2.fastq.gz,0:76 1:76,A:788885030;C:743206390;G:779938637;T:769114909;N:12983602,76,76,,,788885030,743206390,779938637,769114909,12983602,SRX3058778,SRS2404533,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.45295,0.45728,0.06671,0.06598,0.81389,0.81213,0.48974,0.48842,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48370,SRR5893068,SRX3058777,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.1,AG00730.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.1_R1.fastq.gz AG00730.1_R2.fastq.gz,fastq fastq,788630112.0,5188356.0,AG00730.1 R1.fastq.gz,0:76 1:76,A:241944426;C:145730020;G:152521090;T:246715939;N:1718637,76,76,,,241944426,145730020,152521090,246715939,1718637,SRX3058777,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.72997,0.66601,0.51477,0.46195,0.7611,0.77027,0.48262,0.48514,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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
48372,SRR5893070,SRX3058775,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.3,AG00730.3,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.3_R1.fastq.gz AG00730.3_R2.fastq.gz,fastq fastq,2381566704.0,15668202.0,AG00730.3 R2.fastq.gz,0:76 1:76,A:699742976;C:480758524;G:501871756;T:694897427;N:4296021,76,76,,,699742976,480758524,501871756,694897427,4296021,SRX3058775,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.64984,0.69686,0.44721,0.49461,0.77575,0.7558,0.49124,0.49296,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48373,SRR5893071,SRX3058774,SRS2404536,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,dev timecourse AG00730,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:12|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT TinyLNA430 shield R0 B1,AG00730.2,AG00730.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00730.2_R1.fastq.gz AG00730.2_R2.fastq.gz,fastq fastq,2758536584.0,18148267.0,AG00730.2 R2.fastq.gz,0:76 1:76,A:819274018;C:547358767;G:578250069;T:813046584;N:607146,76,76,,,819274018,547358767,578250069,813046584,607146,SRX3058774,SRS2404536,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.63895,0.70578,0.44175,0.50387,0.76844,0.74988,0.49353,0.49135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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
48375,SRR5893162,SRX3058683,SRS2404571,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT a Am shield pA B1,dev timecourse AG00700,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:9|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am shield pA B1,AG00700.1,AG00700.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00700.1_R1.fastq.gz AG00700.1_R2.fastq.gz,fastq fastq,2276298800.0,14975650.0,AG00700.1 R1.fastq.gz,0:76 1:76,A:608754452;C:529104329;G:527812421;T:608782771;N:1844827,76,76,,,608754452,529104329,527812421,608782771,1844827,SRX3058683,SRS2404571,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.91533,0.91935,0.03891,0.03686,0.78289,0.78281,0.49374,0.49427,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48376,SRR5893163,SRX3058682,SRS2404574,SRP149556,PRJNA473824,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq,PRJNA473824,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.,,,,Developmental timecourse   WT shield R0 B2,dev timecourse AG00685,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:6|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT shield R0 B2,AG00685.2,AG00685.2,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00685.2_R1.fastq.gz AG00685.2_R2.fastq.gz,fastq fastq,1680110568.0,11053359.0,AG00685.2 R2.fastq.gz,0:76 1:76,A:429590606;C:407853081;G:410551734;T:431833883;N:281264,76,76,,,429590606,407853081,410551734,431833883,281264,SRX3058682,SRS2404574,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.80758,0.77739,0.2587,0.25273,0.75162,0.75012,0.49289,0.48814,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
48377,SRR5893164,SRX3058681,SRS2404572,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 64c pA B1,dev timecourse AG00692,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:7|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am 64c pA B1,AG00692.1,AG00692.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00692.1_R1.fastq.gz AG00692.1_R2.fastq.gz,fastq fastq,1769692528.0,11642714.0,AG00692.1 R1.fastq.gz,0:76 1:76,A:473892393;C:411257494;G:409923797;T:473090107;N:1528737,76,76,,,473892393,411257494,409923797,473090107,1528737,SRX3058681,SRS2404572,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.91805,0.92435,0.02685,0.02528,0.76903,0.76893,0.49124,0.48516,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
48378,SRR5893165,SRX3058680,SRS2404575,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 64c pA B2,dev timecourse AG00693,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:7|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Developmental timecourse   WT a Am 64c pA B2,AG00693.1,AG00693.1,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP149556,,,AG00693.1_R1.fastq.gz AG00693.1_R2.fastq.gz,fastq fastq,2431950600.0,15999675.0,AG00693.1 R1.fastq.gz,0:76 1:76,A:649992656;C:564963471;G:562148972;T:652726417;N:2119084,76,76,,,649992656,564963471,562148972,652726417,2119084,SRX3058680,SRS2404575,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.92915,0.93349,0.02655,0.02536,0.76469,0.76556,0.48791,0.48893,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures