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81 rows where experiment.library_selection = "unspecified", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Whole Organism"

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devstage_curation 6

technology 2

experiment.library_strategy 2

experiment.library_layout 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 81 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 81 ✖

experiment.library_selection 1

  • unspecified · 81 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
8056 8056 ERR022486 ERX008922 ERS012705 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 1 dpf 2 SAMEA898401 Wellcome Sanger Institute Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 1 dpf RNA from Zebrafish embryo 1 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_3.srf srf 4788693120.0 31504560.0 E MTAB 434:5141 3.srf 0:76 1:76 A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244 76 76     1329328273 1071568772 1063807333 1316891498 7097244 ERX008922 ERS012705 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.95867 0.95691 0.14543 0.14805 0.69753 0.70078 0.46273 0.47662 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Pharyngula Embryo Whole Organism All anatomical structures
8057 8057 ERR022488 ERX008921 ERS012706 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 3 dpf 2 SAMEA898404 Wellcome Sanger Institute Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 3 dpf RNA from Zebrafish embryo 3 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_6.srf srf 3787933176.0 24920613.0 E MTAB 434:5141 6.srf 0:76 1:76 A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818 76 76     1051092006 842721213 838644314 1048667825 6807818 ERX008921 ERS012706 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.95952 0.95914 0.16277 0.16553 0.66352 0.6661 0.46603 0.46879 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Larval Larval Whole Organism All anatomical structures
8058 8058 ERR022485 ERX008920 ERS017423 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 434:ZF 6hpf SAMEA898399 Wellcome Sanger Institute Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 6hpf RNA from Zebrafish embryo 6hpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 4946_6.srf srf 5910514528.0 38884964.0 E MTAB 434:4946 6.srf 0:76 1:76 A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807 76 76     1741038828 1243493514 1214904056 1703863323 7214807 ERX008920 ERS017423 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.91619 0.91684 0.14961 0.15221 0.77189 0.7723 0.49092 0.49303 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-03-10 Gastrula Embryo Whole Organism All anatomical structures
8061 8061 ERR022482 ERX008919 ERS000084 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         5 dpf sample1 SAMEA708828 Wellcome Sanger Institute Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 5 dpf RNA from Zebrafish embryo 5 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 2719_7.srf srf 1764668160.0 16339520.0 E MTAB 434:2719 7.srf 0:54 1:54 A:470580161;C:399075336;G:417290042;T:474450367;N:3272254 54 54     470580161 399075336 417290042 474450367 3272254 ERX008919 ERS000084 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.9454 0.94288 0.20211 0.2029 0.66856 0.67207 0.4856 0.48119 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Larval Larval Whole Organism All anatomical structures
8062 8062 ERR022483 ERX008919 ERS000084 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         5 dpf sample1 SAMEA708828 Wellcome Sanger Institute Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 5 dpf RNA from Zebrafish embryo 5 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 2719_8.srf srf 1678321188.0 15540011.0 E MTAB 434:2719 8.srf 0:54 1:54 A:446988405;C:380486018;G:396533911;T:451117596;N:3195258 54 54     446988405 380486018 396533911 451117596 3195258 ERX008919 ERS000084 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.94565 0.94277 0.19929 0.19877 0.66584 0.67014 0.47973 0.46826 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Larval Larval Whole Organism All anatomical structures
8063 8063 ERR022487 ERX008918 ERS012707 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 2 dpf 2 SAMEA898403 Wellcome Sanger Institute Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 2 dpf RNA from Zebrafish embryo 2 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:2 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_5.srf srf 4321796696.0 28432873.0 E MTAB 434:5141 5.srf 0:76 1:76 A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424 76 76     1185782721 976784015 973264244 1178952292 7013424 ERX008918 ERS012707 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.96001 0.95851 0.15373 0.15636 0.69051 0.69576 0.47409 0.47525 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Hatching Embryo Whole Organism All anatomical structures
36761 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 39751 SRR2422954 SRX1092140 SRS987764 SRP060685 PRJNA289590 Danio rerio Raw sequence reads PRJNA289590 Whole Genome Sequencing The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish     U2AFAB KD U2AFA2B KD U2A2FA and U2AF2B knockdown   treatment:U2AF2A B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 U2AF2A and U2AF2B KD U2AFAB KD 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP060685     zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz fastq fastq 4010033906.0 19851653.0 u2afa u2afb kd 0:101 1:101 A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449 101 101     954988404 1049486839 1028325376 975960838 1272449 SRX1092140 SRS987764 SRA276795 Brown University|Fairbrother Lab Brown University 2 0.88891 0.88704 0.22441 0.2245 0.73781 0.74111 0.60755 0.61314 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-19 Pharyngula Embryo Whole Organism All anatomical structures
39752 39752 SRR2422968 SRX1092139 SRS987762 SRP060685 PRJNA289590 Danio rerio Raw sequence reads PRJNA289590 Whole Genome Sequencing The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish     U2AFB KD U2AF2B KD U2AF2B knockdown   treatment:U2AF2B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 U2AF2B KD U2AFB KD 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP060685     zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz fastq fastq 3657236866.0 18105133.0 u2af2b kd 0:101 1:101 A:859906359;C:963846892;G:950183263;T:882292781;N:1007571 101 101     859906359 963846892 950183263 882292781 1007571 SRX1092139 SRS987762 SRA276795 Brown University|Fairbrother Lab Brown University 2 0.87685 0.87325 0.21282 0.21347 0.74899 0.75166 0.65013 0.65163 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-19 Pharyngula Embryo Whole Organism All anatomical structures
39753 39753 SRR2422941 SRX1092136 SRS987760 SRP060685 PRJNA289590 Danio rerio Raw sequence reads PRJNA289590 Whole Genome Sequencing The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish     Control1 Control1 Control1   treatment:Control 1|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 control 1 Control1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP060685     zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz fastq fastq 5446154724.0 26961162.0 control1 0:101 1:101 A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287 101 101     1236792250 1484635192 1463483173 1259686822 1557287 SRX1092136 SRS987760 SRA276795 Brown University|Fairbrother Lab Brown University 2 0.88645 0.88416 0.23061 0.23167 0.75872 0.75921 0.63459 0.63891 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-19 Pharyngula Embryo Whole Organism All anatomical structures
39754 39754 SRR2422967 SRX1092138 SRS987763 SRP060685 PRJNA289590 Danio rerio Raw sequence reads PRJNA289590 Whole Genome Sequencing The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish     U2AFA KD U2AF2A KD U2AF2A knockdown   treatment:U2AF2A morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 U2AF A KD U2AFA KD 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP060685     zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz fastq fastq 7385905174.0 36563887.0 u2af2a kd 0:101 1:101 A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609 101 101     1742999157 1956220866 1920103000 1764198542 2383609 SRX1092138 SRS987763 SRA276795 Brown University|Fairbrother Lab Brown University 2 0.74404 0.74051 0.14971 0.14762 0.76641 0.76757 0.56197 0.56515 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-19 Pharyngula Embryo Whole Organism All anatomical structures
39755 39755 SRR2422942 SRX1092137 SRS987761 SRP060685 PRJNA289590 Danio rerio Raw sequence reads PRJNA289590 Whole Genome Sequencing The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish     Control2 Control2 Control2   treatment:Control 2|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 control 2 Control 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP060685     zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz fastq fastq 4226478926.0 20923163.0 control2 0:101 1:101 A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890 101 101     1005765442 1098720686 1084955814 1035764094 1272890 SRX1092137 SRS987761 SRA276795 Brown University|Fairbrother Lab Brown University 2 0.83225 0.83092 0.22325 0.22374 0.75396 0.75603 0.6203 0.61868 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-19 Pharyngula Embryo Whole Organism All anatomical structures
39934 39934 SRR2473238 SRX1270438 SRS1078341 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.     Danio rerio embryos ectopically expressing human SPOPwt.   Danio rerio ectopic SPOPwt   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 SPOP mutation leads to genomic instability in prostate cancer Danio rerio ectopic SPOPwt 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz fastq fastq 6185345892.0 60640646.0 Danio rerio ectopic SPOPwt 0:51 1:51 A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809 51 51     1647678166 1462773970 1416249443 1657464504 1179809 SRX1270438 SRS1078341     Weill Cornell Medical College 2 0.94598 0.94553 0.09216 0.0934 0.68789 0.69065 0.46814 0.47172 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2016-02-17 Pharyngula Embryo Whole Organism All anatomical structures
39935 39935 SRR2473236 SRX1270437 SRS1078340 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.     Danio rerio ectopically expressing SPOP F133V   Danio rerio ectopic SPOP F133V   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 SPOP mutation leads to genomic instability in prostate cancer Danio rerio ectopic SPOP F133V 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz fastq fastq 6130528134.0 60103217.0 Danio rerio ectopic SPOP F133V 0:51 1:51 A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035 51 51     1630145057 1450811256 1409924927 1638457859 1189035 SRX1270437 SRS1078340     Weill Cornell Medical College 2 0.9444 0.94139 0.09809 0.0979 0.68487 0.68657 0.46751 0.47276 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-21 Pharyngula Embryo Whole Organism All anatomical structures
39936 39936 SRR2473235 SRX1270436 SRS1078339 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.         Danio rerio SPOP morpholino   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 Danio rerio SPOP morpholino Danio rerio SPOP morpholino 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz fastq fastq 5693947938.0 55823019.0 Danio rerio SPOP morpholino 0:51 1:51 A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641 51 51     1513477521 1350461483 1305374194 1523527099 1107641 SRX1270436 SRS1078339     Weill Cornell Medical College 2 0.94534 0.94431 0.09368 0.0945 0.68941 0.69077 0.46543 0.46749 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2016-02-17 Pharyngula Embryo Whole Organism All anatomical structures
40711 40711 SRR3420419 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz fastq fastq 2419781176.0 15919613.0 AG00719 run 1 0:76 1:76 A:738997601;C:465047900;G:477140497;T:733241052;N:5354126 76 76     738997601 465047900 477140497 733241052 5354126 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.78184 0.71182 0.66469 0.60037 0.75743 0.77518 0.53432 0.52801 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40712 40712 SRR3420420 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz fastq fastq 3074724552.0 20228451.0 AG00719 run 2 0:76 1:76 A:918671897;C:609510609;G:622542852;T:922439528;N:1559666 76 76     918671897 609510609 622542852 922439528 1559666 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76444 0.65488 0.65157 0.55185 0.75741 0.78106 0.53067 0.52622 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40713 40713 SRR3420421 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz fastq fastq 2666395856.0 17542078.0 AG00719 run 3 0:76 1:76 A:787508876;C:539791618;G:549145516;T:785088342;N:4861504 76 76     787508876 539791618 549145516 785088342 4861504 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.75479 0.69465 0.63843 0.58422 0.75716 0.78423 0.53952 0.52615 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40714 40714 SRR3420388 SRX1660356 SRS1360315 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00718 8h 1   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00718 8h 1 AG00718 8h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz fastq fastq 2699903800.0 17762525.0 AG00718 run 1 0:76 1:76 A:832300161;C:503956886;G:525141498;T:832566681;N:5938574 76 76     832300161 503956886 525141498 832566681 5938574 SRX1660356 SRS1360315 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76651 0.69033 0.63937 0.56749 0.77145 0.78545 0.53429 0.53165 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40715 40715 SRR3420392 SRX1660356 SRS1360315 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00718 8h 1   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00718 8h 1 AG00718 8h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz fastq fastq 2798947456.0 18414128.0 AG00718 run 2 0:76 1:76 A:853546590;C:536347349;G:556751964;T:851863324;N:438229 76 76     853546590 536347349 556751964 851863324 438229 SRX1660356 SRS1360315 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74665 0.63683 0.6265 0.5237 0.76134 0.7905 0.54613 0.53982 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40716 40716 SRR3420398 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz fastq fastq 1442918520.0 9492885.0 AG00717 run 1 0:76 1:76 A:442675510;C:273265985;G:284514997;T:439403136;N:3058892 76 76     442675510 273265985 284514997 439403136 3058892 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76736 0.69048 0.60693 0.53532 0.74647 0.76138 0.51546 0.5135 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40717 40717 SRR3420402 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz fastq fastq 2524099688.0 16605919.0 AG00717 run 2 0:76 1:76 A:752163917;C:500880325;G:526291920;T:744462824;N:300702 76 76     752163917 500880325 526291920 744462824 300702 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.7274 0.651 0.57791 0.50498 0.74434 0.76329 0.51831 0.50479 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40718 40718 SRR3420405 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz fastq fastq 1320586032.0 8688066.0 AG00717 run 3 0:76 1:76 A:394339370;C:259687848;G:270914284;T:389960707;N:5683823 76 76     394339370 259687848 270914284 389960707 5683823 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.72219 0.6734 0.55665 0.5122 0.75371 0.76323 0.5098 0.50658 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40719 40719 SRR3420409 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz fastq fastq 1778143272.0 11698311.0 AG00717 run 4 0:76 1:76 A:531893644;C:351009327;G:366187476;T:528937189;N:115636 76 76     531893644 351009327 366187476 528937189 115636 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.72027 0.6573 0.57252 0.50814 0.74913 0.77479 0.51537 0.50066 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40720 40720 SRR3420315 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz fastq fastq 1837024424.0 12085687.0 AG00716 run 1 0:76 1:76 A:571581150;C:339887376;G:357200726;T:564453542;N:3901630 76 76     571581150 339887376 357200726 564453542 3901630 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.77818 0.69777 0.64211 0.56481 0.75503 0.76926 0.50584 0.51507 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40721 40721 SRR3420319 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz fastq fastq 2763994600.0 18184175.0 AG00716 run 2 0:76 1:76 A:841712204;C:530711238;G:562110067;T:828853061;N:608030 76 76     841712204 530711238 562110067 828853061 608030 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74716 0.66787 0.61425 0.53764 0.7475 0.76518 0.50855 0.51311 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40722 40722 SRR3420323 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz fastq fastq 1055704904.0 6945427.0 AG00716 run 3 0:76 1:76 A:323142351;C:199674907;G:210508599;T:317806564;N:4572483 76 76     323142351 199674907 210508599 317806564 4572483 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.73664 0.68701 0.59387 0.5447 0.76179 0.76132 0.51299 0.51552 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40723 40723 SRR3420327 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz fastq fastq 2526928408.0 16624529.0 AG00716 run 4 0:76 1:76 A:771333886;C:482964782;G:508687112;T:763609426;N:333202 76 76     771333886 482964782 508687112 763609426 333202 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74535 0.66478 0.61452 0.53584 0.75826 0.77329 0.51139 0.51539 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40724 40724 SRR3420333 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz fastq fastq 2314408088.0 15226369.0 AG00715 run 1 0:76 1:76 A:652783335;C:485705748;G:507451689;T:663544778;N:4922538 76 76     652783335 485705748 507451689 663544778 4922538 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.59859 0.55293 0.24175 0.21943 0.78384 0.79174 0.52173 0.52111 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40725 40725 SRR3420337 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz fastq fastq 2461668424.0 16195187.0 AG00715 run 2 0:76 1:76 A:653884256;C:562168304;G:597853484;T:647470498;N:291882 76 76     653884256 562168304 597853484 647470498 291882 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.5374 0.51402 0.2167 0.19427 0.78575 0.7934 0.52714 0.53043 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40726 40726 SRR3420341 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz fastq fastq 3692351624.0 24291787.0 AG00715 run 3 0:76 1:76 A:984283909;C:835828915;G:881112020;T:975490829;N:15635951 76 76     984283909 835828915 881112020 975490829 15635951 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.54752 0.52404 0.18037 0.16908 0.79358 0.7961 0.50982 0.50975 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40727 40727 SRR3420346 SRX1660346 SRS1360308 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00714 4h 1   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal                 AG00714 4h 1 AG00714 4h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz fastq fastq 2377192296.0 15639423.0 AG00714 run 1 0:76 1:76 A:694380135;C:473427723;G:496920379;T:707435115;N:5028944 76 76     694380135 473427723 496920379 707435115 5028944 SRX1660346 SRS1360308 SRA395141 Yale University|Giraldez Lab Yale University 2 0.69444 0.63521 0.40011 0.36148 0.76252 0.77116 0.50751 0.5108 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40728 40728 SRR3420349 SRX1660346 SRS1360308 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00714 4h 1   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal                 AG00714 4h 1 AG00714 4h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz fastq fastq 1841902256.0 12117778.0 AG00714 run 2 0:76 1:76 A:517451432;C:392444197;G:415696773;T:508506741;N:7803113 76 76     517451432 392444197 415696773 508506741 7803113 SRX1660346 SRS1360308 SRA395141 Yale University|Giraldez Lab Yale University 2 0.63625 0.60304 0.3341 0.31189 0.77224 0.77703 0.50754 0.51039 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40729 40729 SRR3420359 SRX1660342 SRS1360312 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00713 3h 2   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal                 AG00713 3h 2 AG00713 3h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz fastq fastq 2674764976.0 17597138.0 AG00713 run 1 0:76 1:76 A:738399424;C:560443522;G:578733188;T:791450319;N:5738523 76 76     738399424 560443522 578733188 791450319 5738523 SRX1660342 SRS1360312 SRA395141 Yale University|Giraldez Lab Yale University 2 0.63595 0.60509 0.17579 0.17695 0.79066 0.79815 0.49657 0.4916 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40730 40730 SRR3420362 SRX1660342 SRS1360312 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00713 3h 2   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal                 AG00713 3h 2 AG00713 3h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz fastq fastq 2463895376.0 16209838.0 AG00713 run 2 0:76 1:76 A:661360403;C:556078326;G:581335469;T:654625128;N:10496050 76 76     661360403 556078326 581335469 654625128 10496050 SRX1660342 SRS1360312 SRA395141 Yale University|Giraldez Lab Yale University 2 0.58767 0.56878 0.14864 0.14485 0.79476 0.79898 0.49508 0.49769 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40731 40731 SRR3420369 SRX1660341 SRS1360313 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00712 3h 1   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal                 AG00712 3h 1 AG00712 3h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz fastq fastq 1354427464.0 8910707.0 AG00712 run 1 0:76 1:76 A:382647488;C:281900295;G:291990859;T:395032379;N:2856443 76 76     382647488 281900295 291990859 395032379 2856443 SRX1660341 SRS1360313 SRA395141 Yale University|Giraldez Lab Yale University 2 0.64156 0.60052 0.23835 0.22296 0.78025 0.78717 0.49813 0.49898 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40732 40732 SRR3420375 SRX1660341 SRS1360313 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00712 3h 1   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal                 AG00712 3h 1 AG00712 3h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz fastq fastq 2335782480.0 15366990.0 AG00712 run 2 0:76 1:76 A:638971995;C:517112038;G:538588809;T:640731763;N:377875 76 76     638971995 517112038 538588809 640731763 377875 SRX1660341 SRS1360313 SRA395141 Yale University|Giraldez Lab Yale University 2 0.60525 0.56571 0.24772 0.21069 0.77043 0.78543 0.50862 0.50386 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40733 40733 SRR3420379 SRX1660340 SRS1360314 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00711 2.5h 2   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00711 2.5h 2 AG00711 2.5h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz fastq fastq 2343343264.0 15416732.0 AG00711 run 1 0:76 1:76 A:645206414;C:505367235;G:523792864;T:663977432;N:4999319 76 76     645206414 505367235 523792864 663977432 4999319 SRX1660340 SRS1360314 SRA395141 Yale University|Giraldez Lab Yale University 2 0.59395 0.56211 0.10259 0.10243 0.80598 0.80911 0.51352 0.53772 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40734 40734 SRR3420383 SRX1660340 SRS1360314 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00711 2.5h 2   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00711 2.5h 2 AG00711 2.5h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz fastq fastq 2668460776.0 17555663.0 AG00711 run 2 0:76 1:76 A:709820753;C:602900273;G:626554840;T:717828006;N:11356904 76 76     709820753 602900273 626554840 717828006 11356904 SRX1660340 SRS1360314 SRA395141 Yale University|Giraldez Lab Yale University 2 0.56281 0.54232 0.09217 0.09047 0.80657 0.81018 0.50757 0.52507 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40735 40735 SRR3420304 SRX1660339 SRS1360299 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00710 2.5h 1   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00710 2.5h 1 AG00710 2.5h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz fastq fastq 2705199784.0 17797367.0 AG00710 run 1 0:76 1:76 A:737065338;C:573787464;G:595216660;T:793361986;N:5768336 76 76     737065338 573787464 595216660 793361986 5768336 SRX1660339 SRS1360299 SRA395141 Yale University|Giraldez Lab Yale University 2 0.60426 0.58122 0.08196 0.09224 0.80578 0.8075 0.50121 0.50121 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40736 40736 SRR3420308 SRX1660339 SRS1360299 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00710 2.5h 1   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00710 2.5h 1 AG00710 2.5h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz fastq fastq 2275540168.0 14970659.0 AG00710 run 2 0:76 1:76 A:614429428;C:505827101;G:528906356;T:616697803;N:9679480 76 76     614429428 505827101 528906356 616697803 9679480 SRX1660339 SRS1360299 SRA395141 Yale University|Giraldez Lab Yale University 2 0.57792 0.56382 0.07268 0.07246 0.80261 0.80612 0.49743 0.50296 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
52829 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 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 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 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 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 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
54188 54188 SRR10095964 SRX6828145 SRS5370320 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         5b   strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 5b 5b 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 90080193105.0 566542095.0 5b.gz 0:26 1:133 A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734 26 133     25143336916 20071432223 20537826191 24313961041 13636734 SRX6828145 SRS5370320 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.00976 0.95301 0.00215 0.10077 0.97926 0.77851 0.44407 0.5221 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Larval Larval Whole Organism All anatomical structures
54189 54189 SRR10095965 SRX6828144 SRS5370319 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         5a   strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 5a 5a 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 106640540616.0 670695224.0 5a.gz 0:26 1:133 A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145 26 133     29532468637 23968826821 24791831474 28331248539 16165145 SRX6828144 SRS5370319 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.01014 0.95016 0.00222 0.09527 0.97855 0.78212 0.41929 0.50263 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Larval Larval Whole Organism All anatomical structures
54190 54190 SRR10095966 SRX6828143 SRS5370318 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         2b   strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 2b 2b 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 100194025377.0 630151103.0 2b.gz 0:26 1:133 A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462 26 133     27235389395 22388810842 23041272930 27513445748 15106462 SRX6828143 SRS5370318 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.0127 0.95456 0.00215 0.09469 0.97463 0.79308 0.43287 0.50046 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Hatching Embryo Whole Organism All anatomical structures
54191 54191 SRR10095967 SRX6828142 SRS5370317 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         2a   strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 2a 2a 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA NextSeq 500   SRP221273   loader:latf load 2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 30654488793.0 192795527.0 2a.gz 0:26 1:133 A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245 26 133     8922702024 6370087682 7321183700 8019014142 21501245 SRX6828142 SRS5370317 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.00427 0.91705 0.00106 0.08701 0.98999 0.8198 0.35255 0.50555 26 133 T B sc-like readlen illumina nextseq unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Hatching Embryo Whole Organism All anatomical structures
54192 54192 SRR10095968 SRX6828141 SRS5370316 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         1b   strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 1b 1b 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 98193351273.0 617568247.0 1b.gz 0:26 1:133 A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797 26 133     27237053473 21828277485 22951157364 26162156154 14706797 SRX6828141 SRS5370316 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.01479 0.95138 0.00273 0.12104 0.97327 0.78293 0.39405 0.4998 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Pharyngula Embryo Whole Organism All anatomical structures
54193 54193 SRR10095969 SRX6828140 SRS5370315 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         1a   strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1a|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 1a 1a 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 99552249225.0 626114775.0 1a.gz 0:26 1:133 A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522 26 133     27540748865 22111148705 23108024457 26777444676 14882522 SRX6828140 SRS5370315 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.01166 0.95413 0.002 0.08635 0.9779 0.80034 0.44044 0.48046 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Pharyngula Embryo Whole Organism All anatomical structures
74579 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 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 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 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 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 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 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 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 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 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 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 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

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