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219 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "unspecified" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation 9

tissue_curation 2

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devstage_curation_coarse 2

tissue_curation_coarse 1

  • All anatomical structures · 219 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 219 ✖

experiment.library_layout 1

  • PAIRED · 219 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;