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
8056,ERR022486,ERX008922,ERS012705,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 1 dpf,RNA from Zebrafish embryo 1 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_3.srf,srf,4788693120.0,31504560.0,E MTAB 434:5141 3.srf,0:76 1:76,A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244,76,76,,,1329328273,1071568772,1063807333,1316891498,7097244,ERX008922,ERS012705,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95867,0.95691,0.14543,0.14805,0.69753,0.70078,0.46273,0.47662,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
8057,ERR022488,ERX008921,ERS012706,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 3 dpf 2,SAMEA898404,Wellcome Sanger Institute,Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 3 dpf,RNA from Zebrafish embryo 3 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_6.srf,srf,3787933176.0,24920613.0,E MTAB 434:5141 6.srf,0:76 1:76,A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818,76,76,,,1051092006,842721213,838644314,1048667825,6807818,ERX008921,ERS012706,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95952,0.95914,0.16277,0.16553,0.66352,0.6661,0.46603,0.46879,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
8058,ERR022485,ERX008920,ERS017423,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 6hpf,SAMEA898399,Wellcome Sanger Institute,Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 6hpf,RNA from Zebrafish embryo 6hpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_6.srf,srf,5910514528.0,38884964.0,E MTAB 434:4946 6.srf,0:76 1:76,A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807,76,76,,,1741038828,1243493514,1214904056,1703863323,7214807,ERX008920,ERS017423,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.91619,0.91684,0.14961,0.15221,0.77189,0.7723,0.49092,0.49303,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Gastrula,Embryo,Whole Organism,All anatomical structures
8061,ERR022482,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_7.srf,srf,1764668160.0,16339520.0,E MTAB 434:2719 7.srf,0:54 1:54,A:470580161;C:399075336;G:417290042;T:474450367;N:3272254,54,54,,,470580161,399075336,417290042,474450367,3272254,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.9454,0.94288,0.20211,0.2029,0.66856,0.67207,0.4856,0.48119,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8062,ERR022483,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_8.srf,srf,1678321188.0,15540011.0,E MTAB 434:2719 8.srf,0:54 1:54,A:446988405;C:380486018;G:396533911;T:451117596;N:3195258,54,54,,,446988405,380486018,396533911,451117596,3195258,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94565,0.94277,0.19929,0.19877,0.66584,0.67014,0.47973,0.46826,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8063,ERR022487,ERX008918,ERS012707,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 2 dpf 2,SAMEA898403,Wellcome Sanger Institute,Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2 dpf,RNA from Zebrafish embryo 2 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:2 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_5.srf,srf,4321796696.0,28432873.0,E MTAB 434:5141 5.srf,0:76 1:76,A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424,76,76,,,1185782721,976784015,973264244,1178952292,7013424,ERX008918,ERS012707,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96001,0.95851,0.15373,0.15636,0.69051,0.69576,0.47409,0.47525,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Hatching,Embryo,Whole Organism,All anatomical structures
36761,SRR10295266,SRX7008094,SRS431105,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT 2hpf Total mRNA,GSM1152440,,source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,,,,,,,,,WT 64c R0,AGR000324,AGR000324,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,AGR000324_R1.fastq.gz,fastq,781504124.0,10282949.0,AGR000324 R1.fastq.gz,0:76,A:151879560;C:240178928;G:220957551;T:168456166;N:31919,76,,,,151879560,240178928,220957551,168456166,31919,SRX7008094,SRS431105,SRA980383,Yale_Giraldez|Genetics,"Giraldez Lab, Genetics, Yale University",1,0.88875,,0.14141,,0.796,,0.72154,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-10-16,Cleavage,Embryo,Whole Organism,All anatomical structures
39687,SRR2051113,SRX1048368,SRS952733,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P39,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 4,P39,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4090297192.0,40497992.0,P39,0:101,A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421,101,,,,1016157993,993771683,965986507,1113686588,694421,SRX1048368,SRS952733,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9417,,0.14428,,0.68937,,0.5438,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39688,SRR2051110,SRX1048367,SRS952731,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P37,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 3,P37,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4647442886.0,46014286.0,P37,0:101,A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479,101,,,,1149955739,1129088798,1093234722,1274375148,788479,SRX1048367,SRS952731,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94585,,0.12571,,0.68633,,0.52597,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39689,SRR2051112,SRX1048366,SRS952732,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P36,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 2,P36,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4296894611.0,42543511.0,P36,0:101,A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407,101,,,,1050039699,1061123166,1022913715,1162094624,723407,SRX1048366,SRS952732,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94977,,0.13188,,0.70976,,0.52728,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39690,SRR2051109,SRX1048365,SRS952730,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P35,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 1,P35,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4094752706.0,40542106.0,P35,0:101,A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167,101,,,,1009779802,1004374749,969241794,1110655194,701167,SRX1048365,SRS952730,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94442,,0.13203,,0.70023,,0.53953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39691,SRR2051102,SRX1048364,SRS952729,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P29,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 4,P29,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4983571896.0,49342296.0,P29,0:101,A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841,101,,,,1247122516,1202173111,1173654831,1359775597,845841,SRX1048364,SRS952729,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94329,,0.13234,,0.68286,,0.51586,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39692,SRR2051100,SRX1048363,SRS952727,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P28,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 3,P28,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4032678914.0,39927514.0,P28,0:101,A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488,101,,,,1015356577,970369004,937306142,1108957703,689488,SRX1048363,SRS952727,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93887,,0.13869,,0.69079,,0.52237,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39693,SRR2051101,SRX1048362,SRS952728,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P26,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 2,P26,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz,fastq fastq fastq fastq,6526758875.0,64621375.0,P26,0:101,A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228,101,,,,1635664768,1568967965,1518148006,1802863908,1114228,SRX1048362,SRS952728,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93822,,0.15203,,0.68609,,0.53171,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39694,SRR2051096,SRX1048361,SRS952726,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P25,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 1,P25,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4185957322.0,41445122.0,P25,0:101,A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428,101,,,,1081936223,978799105,956795307,1167714259,712428,SRX1048361,SRS952726,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9288,,0.17032,,0.6801,,0.51298,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39695,SRR2051095,SRX1048360,SRS952725,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P19,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 4,P19,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4293546461.0,42510361.0,P19,0:101,A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822,101,,,,1062707728,1045602693,1011860446,1172670772,704822,SRX1048360,SRS952725,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94381,,0.13697,,0.69051,,0.51415,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39696,SRR2051094,SRX1048359,SRS952724,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P18,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 3,P18,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4257944163.0,42157863.0,P18,0:101,A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125,101,,,,1044532409,1049992329,1010166097,1152524203,729125,SRX1048359,SRS952724,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94262,,0.14592,,0.69014,,0.52498,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39697,SRR2051093,SRX1048358,SRS952723,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P17,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 2,P17,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4278385553.0,42360253.0,P17,0:101,A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139,101,,,,1040955882,1060023973,1019487833,1157186726,731139,SRX1048358,SRS952723,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94697,,0.14458,,0.69643,,0.53451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39698,SRR2051092,SRX1048357,SRS952722,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P15,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 1,P15,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4341747499.0,42987599.0,P15,0:101,A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377,101,,,,1052621077,1088380866,1041958433,1158051746,735377,SRX1048357,SRS952722,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94563,,0.153,,0.69822,,0.54133,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39699,SRR2051091,SRX1048356,SRS952721,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN9,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 4,CN9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4220387212.0,41786012.0,CN9,0:101,A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235,101,,,,1031722430,1044497851,1005706674,1137783022,677235,SRX1048356,SRS952721,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.95231,,0.14084,,0.69682,,0.52966,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39700,SRR2051090,SRX1048354,SRS952719,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN8,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 3,CN8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,5835502553.0,57777253.0,CN8,0:101,A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739,101,,,,1424369529,1441755207,1391851806,1576540272,985739,SRX1048354,SRS952719,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94643,,0.12925,,0.70725,,0.52949,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39701,SRR2050894,SRX1048353,SRS952718,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN7,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 2,CN7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4789094477.0,47416777.0,CN7,0:101,A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016,101,,,,1160528098,1197558725,1155573375,1274638263,796016,SRX1048353,SRS952718,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9501,,0.14828,,0.69966,,0.52764,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39702,SRR2050892,SRX1048352,SRS952717,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN5,,breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 1,CN5,CN5 EL4506 TGACCA,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4526144512.0,44813312.0,CN5,0:101,A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159,101,,,,1109966549,1116619353,1075422479,1223366972,769159,SRX1048352,SRS952717,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94604,,0.14084,,0.69004,,0.53407,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39751,SRR2422954,SRX1092140,SRS987764,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFAB KD,U2AFA2B KD,U2A2FA and U2AF2B knockdown,,treatment:U2AF2A B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2A and U2AF2B KD,U2AFAB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz,fastq fastq,4010033906.0,19851653.0,u2afa u2afb kd,0:101 1:101,A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449,101,101,,,954988404,1049486839,1028325376,975960838,1272449,SRX1092140,SRS987764,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88891,0.88704,0.22441,0.2245,0.73781,0.74111,0.60755,0.61314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39752,SRR2422968,SRX1092139,SRS987762,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFB KD,U2AF2B KD,U2AF2B knockdown,,treatment:U2AF2B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2B KD,U2AFB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz,fastq fastq,3657236866.0,18105133.0,u2af2b kd,0:101 1:101,A:859906359;C:963846892;G:950183263;T:882292781;N:1007571,101,101,,,859906359,963846892,950183263,882292781,1007571,SRX1092139,SRS987762,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.87685,0.87325,0.21282,0.21347,0.74899,0.75166,0.65013,0.65163,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39753,SRR2422941,SRX1092136,SRS987760,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,Control1,Control1,Control1,,treatment:Control 1|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 1,Control1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz,fastq fastq,5446154724.0,26961162.0,control1,0:101 1:101,A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287,101,101,,,1236792250,1484635192,1463483173,1259686822,1557287,SRX1092136,SRS987760,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88645,0.88416,0.23061,0.23167,0.75872,0.75921,0.63459,0.63891,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39754,SRR2422967,SRX1092138,SRS987763,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,U2AFA KD,U2AF2A KD,U2AF2A knockdown,,treatment:U2AF2A morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF A KD,U2AFA KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz,fastq fastq,7385905174.0,36563887.0,u2af2a kd,0:101 1:101,A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609,101,101,,,1742999157,1956220866,1920103000,1764198542,2383609,SRX1092138,SRS987763,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.74404,0.74051,0.14971,0.14762,0.76641,0.76757,0.56197,0.56515,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39755,SRR2422942,SRX1092137,SRS987761,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression  especially splicing  profiles in wildtype and U2af2 KD zebrafish,,,Control2,Control2,Control2,,treatment:Control 2|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 2,Control 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP060685,,,zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz,fastq fastq,4226478926.0,20923163.0,control2,0:101 1:101,A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890,101,101,,,1005765442,1098720686,1084955814,1035764094,1272890,SRX1092137,SRS987761,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.83225,0.83092,0.22325,0.22374,0.75396,0.75603,0.6203,0.61868,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39934,SRR2473238,SRX1270438,SRS1078341,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio embryos ectopically expressing human SPOPwt.,,Danio rerio ectopic SPOPwt,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOPwt,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz,fastq fastq,6185345892.0,60640646.0,Danio rerio ectopic SPOPwt,0:51 1:51,A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809,51,51,,,1647678166,1462773970,1416249443,1657464504,1179809,SRX1270438,SRS1078341,,,Weill Cornell Medical College,2,0.94598,0.94553,0.09216,0.0934,0.68789,0.69065,0.46814,0.47172,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
39935,SRR2473236,SRX1270437,SRS1078340,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio ectopically expressing SPOP F133V,,Danio rerio ectopic SPOP F133V,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOP F133V,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz,fastq fastq,6130528134.0,60103217.0,Danio rerio ectopic SPOP F133V,0:51 1:51,A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035,51,51,,,1630145057,1450811256,1409924927,1638457859,1189035,SRX1270437,SRS1078340,,,Weill Cornell Medical College,2,0.9444,0.94139,0.09809,0.0979,0.68487,0.68657,0.46751,0.47276,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
39936,SRR2473235,SRX1270436,SRS1078339,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,,,Danio rerio SPOP morpholino,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio SPOP morpholino,Danio rerio SPOP morpholino,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063952,,,Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz,fastq fastq,5693947938.0,55823019.0,Danio rerio SPOP morpholino,0:51 1:51,A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641,51,51,,,1513477521,1350461483,1305374194,1523527099,1107641,SRX1270436,SRS1078339,,,Weill Cornell Medical College,2,0.94534,0.94431,0.09368,0.0945,0.68941,0.69077,0.46543,0.46749,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
40711,SRR3420419,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz,fastq fastq,2419781176.0,15919613.0,AG00719 run 1,0:76 1:76,A:738997601;C:465047900;G:477140497;T:733241052;N:5354126,76,76,,,738997601,465047900,477140497,733241052,5354126,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.78184,0.71182,0.66469,0.60037,0.75743,0.77518,0.53432,0.52801,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40712,SRR3420420,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz,fastq fastq,3074724552.0,20228451.0,AG00719 run 2,0:76 1:76,A:918671897;C:609510609;G:622542852;T:922439528;N:1559666,76,76,,,918671897,609510609,622542852,922439528,1559666,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76444,0.65488,0.65157,0.55185,0.75741,0.78106,0.53067,0.52622,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40713,SRR3420421,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz,fastq fastq,2666395856.0,17542078.0,AG00719 run 3,0:76 1:76,A:787508876;C:539791618;G:549145516;T:785088342;N:4861504,76,76,,,787508876,539791618,549145516,785088342,4861504,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.75479,0.69465,0.63843,0.58422,0.75716,0.78423,0.53952,0.52615,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40714,SRR3420388,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz,fastq fastq,2699903800.0,17762525.0,AG00718 run 1,0:76 1:76,A:832300161;C:503956886;G:525141498;T:832566681;N:5938574,76,76,,,832300161,503956886,525141498,832566681,5938574,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76651,0.69033,0.63937,0.56749,0.77145,0.78545,0.53429,0.53165,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40715,SRR3420392,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz,fastq fastq,2798947456.0,18414128.0,AG00718 run 2,0:76 1:76,A:853546590;C:536347349;G:556751964;T:851863324;N:438229,76,76,,,853546590,536347349,556751964,851863324,438229,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74665,0.63683,0.6265,0.5237,0.76134,0.7905,0.54613,0.53982,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40716,SRR3420398,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz,fastq fastq,1442918520.0,9492885.0,AG00717 run 1,0:76 1:76,A:442675510;C:273265985;G:284514997;T:439403136;N:3058892,76,76,,,442675510,273265985,284514997,439403136,3058892,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76736,0.69048,0.60693,0.53532,0.74647,0.76138,0.51546,0.5135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40717,SRR3420402,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz,fastq fastq,2524099688.0,16605919.0,AG00717 run 2,0:76 1:76,A:752163917;C:500880325;G:526291920;T:744462824;N:300702,76,76,,,752163917,500880325,526291920,744462824,300702,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.7274,0.651,0.57791,0.50498,0.74434,0.76329,0.51831,0.50479,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40718,SRR3420405,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz,fastq fastq,1320586032.0,8688066.0,AG00717 run 3,0:76 1:76,A:394339370;C:259687848;G:270914284;T:389960707;N:5683823,76,76,,,394339370,259687848,270914284,389960707,5683823,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72219,0.6734,0.55665,0.5122,0.75371,0.76323,0.5098,0.50658,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40719,SRR3420409,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz,fastq fastq,1778143272.0,11698311.0,AG00717 run 4,0:76 1:76,A:531893644;C:351009327;G:366187476;T:528937189;N:115636,76,76,,,531893644,351009327,366187476,528937189,115636,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72027,0.6573,0.57252,0.50814,0.74913,0.77479,0.51537,0.50066,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40720,SRR3420315,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz,fastq fastq,1837024424.0,12085687.0,AG00716 run 1,0:76 1:76,A:571581150;C:339887376;G:357200726;T:564453542;N:3901630,76,76,,,571581150,339887376,357200726,564453542,3901630,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.77818,0.69777,0.64211,0.56481,0.75503,0.76926,0.50584,0.51507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40721,SRR3420319,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz,fastq fastq,2763994600.0,18184175.0,AG00716 run 2,0:76 1:76,A:841712204;C:530711238;G:562110067;T:828853061;N:608030,76,76,,,841712204,530711238,562110067,828853061,608030,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74716,0.66787,0.61425,0.53764,0.7475,0.76518,0.50855,0.51311,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40722,SRR3420323,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz,fastq fastq,1055704904.0,6945427.0,AG00716 run 3,0:76 1:76,A:323142351;C:199674907;G:210508599;T:317806564;N:4572483,76,76,,,323142351,199674907,210508599,317806564,4572483,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.73664,0.68701,0.59387,0.5447,0.76179,0.76132,0.51299,0.51552,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40723,SRR3420327,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz,fastq fastq,2526928408.0,16624529.0,AG00716 run 4,0:76 1:76,A:771333886;C:482964782;G:508687112;T:763609426;N:333202,76,76,,,771333886,482964782,508687112,763609426,333202,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74535,0.66478,0.61452,0.53584,0.75826,0.77329,0.51139,0.51539,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40724,SRR3420333,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz,fastq fastq,2314408088.0,15226369.0,AG00715 run 1,0:76 1:76,A:652783335;C:485705748;G:507451689;T:663544778;N:4922538,76,76,,,652783335,485705748,507451689,663544778,4922538,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59859,0.55293,0.24175,0.21943,0.78384,0.79174,0.52173,0.52111,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40725,SRR3420337,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz,fastq fastq,2461668424.0,16195187.0,AG00715 run 2,0:76 1:76,A:653884256;C:562168304;G:597853484;T:647470498;N:291882,76,76,,,653884256,562168304,597853484,647470498,291882,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.5374,0.51402,0.2167,0.19427,0.78575,0.7934,0.52714,0.53043,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40726,SRR3420341,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz,fastq fastq,3692351624.0,24291787.0,AG00715 run 3,0:76 1:76,A:984283909;C:835828915;G:881112020;T:975490829;N:15635951,76,76,,,984283909,835828915,881112020,975490829,15635951,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.54752,0.52404,0.18037,0.16908,0.79358,0.7961,0.50982,0.50975,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40727,SRR3420346,SRX1660346,SRS1360308,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz,fastq fastq,2377192296.0,15639423.0,AG00714 run 1,0:76 1:76,A:694380135;C:473427723;G:496920379;T:707435115;N:5028944,76,76,,,694380135,473427723,496920379,707435115,5028944,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.69444,0.63521,0.40011,0.36148,0.76252,0.77116,0.50751,0.5108,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40728,SRR3420349,SRX1660346,SRS1360308,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz,fastq fastq,1841902256.0,12117778.0,AG00714 run 2,0:76 1:76,A:517451432;C:392444197;G:415696773;T:508506741;N:7803113,76,76,,,517451432,392444197,415696773,508506741,7803113,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63625,0.60304,0.3341,0.31189,0.77224,0.77703,0.50754,0.51039,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40729,SRR3420359,SRX1660342,SRS1360312,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz,fastq fastq,2674764976.0,17597138.0,AG00713 run 1,0:76 1:76,A:738399424;C:560443522;G:578733188;T:791450319;N:5738523,76,76,,,738399424,560443522,578733188,791450319,5738523,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63595,0.60509,0.17579,0.17695,0.79066,0.79815,0.49657,0.4916,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40730,SRR3420362,SRX1660342,SRS1360312,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz,fastq fastq,2463895376.0,16209838.0,AG00713 run 2,0:76 1:76,A:661360403;C:556078326;G:581335469;T:654625128;N:10496050,76,76,,,661360403,556078326,581335469,654625128,10496050,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.58767,0.56878,0.14864,0.14485,0.79476,0.79898,0.49508,0.49769,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40731,SRR3420369,SRX1660341,SRS1360313,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz,fastq fastq,1354427464.0,8910707.0,AG00712 run 1,0:76 1:76,A:382647488;C:281900295;G:291990859;T:395032379;N:2856443,76,76,,,382647488,281900295,291990859,395032379,2856443,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.64156,0.60052,0.23835,0.22296,0.78025,0.78717,0.49813,0.49898,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40732,SRR3420375,SRX1660341,SRS1360313,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz,fastq fastq,2335782480.0,15366990.0,AG00712 run 2,0:76 1:76,A:638971995;C:517112038;G:538588809;T:640731763;N:377875,76,76,,,638971995,517112038,538588809,640731763,377875,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60525,0.56571,0.24772,0.21069,0.77043,0.78543,0.50862,0.50386,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40733,SRR3420379,SRX1660340,SRS1360314,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz,fastq fastq,2343343264.0,15416732.0,AG00711 run 1,0:76 1:76,A:645206414;C:505367235;G:523792864;T:663977432;N:4999319,76,76,,,645206414,505367235,523792864,663977432,4999319,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59395,0.56211,0.10259,0.10243,0.80598,0.80911,0.51352,0.53772,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40734,SRR3420383,SRX1660340,SRS1360314,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz,fastq fastq,2668460776.0,17555663.0,AG00711 run 2,0:76 1:76,A:709820753;C:602900273;G:626554840;T:717828006;N:11356904,76,76,,,709820753,602900273,626554840,717828006,11356904,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.56281,0.54232,0.09217,0.09047,0.80657,0.81018,0.50757,0.52507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40735,SRR3420304,SRX1660339,SRS1360299,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz,fastq fastq,2705199784.0,17797367.0,AG00710 run 1,0:76 1:76,A:737065338;C:573787464;G:595216660;T:793361986;N:5768336,76,76,,,737065338,573787464,595216660,793361986,5768336,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60426,0.58122,0.08196,0.09224,0.80578,0.8075,0.50121,0.50121,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40736,SRR3420308,SRX1660339,SRS1360299,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz,fastq fastq,2275540168.0,14970659.0,AG00710 run 2,0:76 1:76,A:614429428;C:505827101;G:528906356;T:616697803;N:9679480,76,76,,,614429428,505827101,528906356,616697803,9679480,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.57792,0.56382,0.07268,0.07246,0.80261,0.80612,0.49743,0.50296,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
52829,SRR9277355,SRX6047142,SRS4950160,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample04,,dkc1 elu1 mut1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT1,MUT1,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-1_R1.fastq.gz,fastq,2425739178.0,32540543.0,MUT 1 R1.fastq.gz,0:74.55 1:0,A:562954867;C:599474858;G:575980257;T:687194946;N:134250,74,0,,,562954867,599474858,575980257,687194946,134250,SRX6047142,SRS4950160,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.96592,,0.05193,,0.69181,,0.46287,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52830,SRR9277356,SRX6047141,SRS4950159,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample03,,dkc1 elu1 sib3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB3,SIB3,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-3_R1.fastq.gz,fastq,2525161946.0,33921476.0,SIB 3 R1.fastq.gz,0:74.44 1:0,A:617606365;C:576906982;G:574368411;T:756144418;N:135770,74,0,,,617606365,576906982,574368411,756144418,135770,SRX6047141,SRS4950159,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95481,,0.09246,,0.70187,,0.48651,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52831,SRR9277357,SRX6047140,SRS4950158,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample02,,dkc1 elu1 sib2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB2,SIB2,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-2_R1.fastq.gz,fastq,2500753589.0,33594139.0,SIB 2 R1.fastq.gz,0:74.44 1:0,A:594107753;C:588927623;G:585955773;T:731305179;N:457261,74,0,,,594107753,588927623,585955773,731305179,457261,SRX6047140,SRS4950158,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95785,,0.07623,,0.70512,,0.49187,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52832,SRR9277358,SRX6047139,SRS4950157,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample01,,dkc1 elu1 sib1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB1,SIB1,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-1_R1.fastq.gz,fastq,2611643150.0,35032800.0,SIB 1 R1.fastq.gz,0:74.55 1:0,A:594796815;C:658132193;G:620365621;T:738201586;N:146935,74,0,,,594796815,658132193,620365621,738201586,146935,SRX6047139,SRS4950157,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.97084,,0.05106,,0.69858,,0.46901,,73,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52833,SRR9277359,SRX6047138,SRS4950156,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample06,,dkc1 elu1 mut3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT3,MUT3,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-3_R1.fastq.gz,fastq,2503783299.0,33623629.0,MUT 3 R1.fastq.gz,0:74.46 1:0,A:603400760;C:568138093;G:589455352;T:742564020;N:225074,74,0,,,603400760,568138093,589455352,742564020,225074,SRX6047138,SRS4950156,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95328,,0.08246,,0.69581,,0.48805,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52834,SRR9277360,SRX6047137,SRS4950155,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample05,,dkc1 elu1 mut2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT2,MUT2,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-2_R1.fastq.gz,fastq,2437701211.0,32733070.0,MUT 2 R1.fastq.gz,0:74.47 1:0,A:590961375;C:565727869;G:562583560;T:718173630;N:254777,74,0,,,590961375,565727869,562583560,718173630,254777,SRX6047137,SRS4950155,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95589,,0.07601,,0.70317,,0.49704,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
74579,SRR23974542,SRX19779002,SRS17142416,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D1,,isolate:10|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,10,10,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP1F.fq.gz,fastq,2956240050.0,19708267.0,TP1F.fq.gz,0:150 1:0,A:785689496;C:695356949;G:702558232;T:772610474;N:24899,150,0,,,785689496,695356949,702558232,772610474,24899,SRX19779002,SRS17142416,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93915,,0.07675,,0.68534,,0.4891,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74580,SRR23974543,SRX19779001,SRS17142414,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C3,,isolate:9|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,9,9,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP3F.fq.gz,fastq,3243688800.0,21624592.0,CP3F.fq.gz,0:150 1:0,A:866441929;C:744536766;G:783433493;T:849247758;N:28854,150,0,,,866441929,744536766,783433493,849247758,28854,SRX19779001,SRS17142414,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.91011,,0.086,,0.68972,,0.48291,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74581,SRR23974544,SRX19779000,SRS17142415,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C2,,isolate:8|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,8,8,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP2F.fq.gz,fastq,3455536800.0,23036912.0,CP2F.fq.gz,0:150 1:0,A:955162327;C:765147222;G:797594182;T:937601078;N:31991,150,0,,,955162327,765147222,797594182,937601078,31991,SRX19779000,SRS17142415,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90361,,0.13207,,0.69345,,0.48842,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74582,SRR23974545,SRX19778999,SRS17142412,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C1,,isolate:7|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,7,7,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP1F.fq.gz,fastq,3394157850.0,22627719.0,CP1F.fq.gz,0:150 1:0,A:918865518;C:780289302;G:793602009;T:901371269;N:29752,150,0,,,918865518,780289302,793602009,901371269,29752,SRX19778999,SRS17142412,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93417,,0.08314,,0.68006,,0.48695,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74583,SRR23974546,SRX19778998,SRS17142413,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B3,,isolate:6|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,6,6,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE3F.fq.gz,fastq,3021012750.0,20140085.0,TE3F.fq.gz,0:150 1:0,A:802754479;C:697084034;G:736507600;T:784641365;N:25272,150,0,,,802754479,697084034,736507600,784641365,25272,SRX19778998,SRS17142413,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.9039,,0.08388,,0.6997,,0.49603,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74584,SRR23974547,SRX19778997,SRS17142411,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B2,,isolate:5|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,5,5,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE2F.fq.gz,fastq,3037657950.0,20251053.0,TE2F.fq.gz,0:150 1:0,A:806162990;C:709397050;G:731668622;T:790403768;N:25520,150,0,,,806162990,709397050,731668622,790403768,25520,SRX19778997,SRS17142411,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.92641,,0.07865,,0.69798,,0.46929,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74585,SRR23974548,SRX19778996,SRS17142410,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B1,,isolate:4|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,4,4,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE1F.fq.gz,fastq,3459122100.0,23060814.0,TE1F.fq.gz,0:150 1:0,A:957107791;C:768667835;G:795319703;T:937996052;N:30719,150,0,,,957107791,768667835,795319703,937996052,30719,SRX19778996,SRS17142410,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90435,,0.12237,,0.70128,,0.47725,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74586,SRR23974549,SRX19778995,SRS17142409,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A3,,isolate:3|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,3,3,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE3F.fq.gz,fastq,3496645950.0,23310973.0,CE3F.fq.gz,0:150 1:0,A:927418130;C:820945235;G:834908249;T:913344868;N:29468,150,0,,,927418130,820945235,834908249,913344868,29468,SRX19778995,SRS17142409,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93227,,0.08275,,0.69339,,0.49066,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74587,SRR23974550,SRX19778994,SRS17142408,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D3,,isolate:12|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,12,12,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP3F.fq.gz,fastq,3317790150.0,22118601.0,TP3F.fq.gz,0:150 1:0,A:883540292;C:768555339;G:796741351;T:868924072;N:29096,150,0,,,883540292,768555339,796741351,868924072,29096,SRX19778994,SRS17142408,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74588,SRR23974551,SRX19778993,SRS17142407,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D2,,isolate:11|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,11,11,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP2F.fq.gz,fastq,2948738400.0,19658256.0,TP2F.fq.gz,0:150 1:0,A:777218056;C:697066948;G:709846212;T:764582431;N:24753,150,0,,,777218056,697066948,709846212,764582431,24753,SRX19778993,SRS17142407,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74589,SRR23974552,SRX19778992,SRS17142405,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A2,,isolate:2|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,2,2,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE2F.fq.gz,fastq,3760293450.0,25068623.0,CE2F.fq.gz,0:150 1:0,A:1000790271;C:868241486;G:905025923;T:986203921;N:31849,150,0,,,1000790271,868241486,905025923,986203921,31849,SRX19778992,SRS17142405,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74590,SRR23974553,SRX19778991,SRS17142406,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A1,,isolate:1|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,1,1,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE1F.fq.gz,fastq,3446794950.0,22978633.0,CE1F.fq.gz,0:150 1:0,A:916043654;C:787898255;G:842788936;T:900033406;N:30699,150,0,,,916043654,787898255,842788936,900033406,30699,SRX19778991,SRS17142406,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.89022,,0.09813,,0.69954,,0.49171,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures