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275 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "unspecified" and technology = "unknown"

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devstage_curation 10

devstage_curation_coarse 4

experiment.library_strategy 2

technology 1

  • unknown · 275 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 275 ✖

experiment.library_layout 1

  • PAIRED · 275 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
8055 8055 ERR022484 ERX008924 ERS017427 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 434:ZF 2cells SAMEA898400 Wellcome Sanger Institute Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 2cells RNA from Zebrafish embryo 2cells Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 4946_5.srf srf 3947547008.0 25970704.0 E MTAB 434:4946 5.srf 0:76 1:76 A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500 76 76     1069302461 914233601 902631356 1055986090 5393500 ERX008924 ERS017427 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.93356 0.93346 0.03988 0.04022 0.79135 0.79198 0.48864 0.48464 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-03-10 Cleavage Embryo Embryo Imprecise All anatomical structures
8056 8056 ERR022486 ERX008922 ERS012705 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 1 dpf 2 SAMEA898401 Wellcome Sanger Institute Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 1 dpf RNA from Zebrafish embryo 1 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_3.srf srf 4788693120.0 31504560.0 E MTAB 434:5141 3.srf 0:76 1:76 A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244 76 76     1329328273 1071568772 1063807333 1316891498 7097244 ERX008922 ERS012705 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.95867 0.95691 0.14543 0.14805 0.69753 0.70078 0.46273 0.47662 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Pharyngula Embryo Whole Organism All anatomical structures
8057 8057 ERR022488 ERX008921 ERS012706 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 3 dpf 2 SAMEA898404 Wellcome Sanger Institute Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 3 dpf RNA from Zebrafish embryo 3 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_6.srf srf 3787933176.0 24920613.0 E MTAB 434:5141 6.srf 0:76 1:76 A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818 76 76     1051092006 842721213 838644314 1048667825 6807818 ERX008921 ERS012706 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.95952 0.95914 0.16277 0.16553 0.66352 0.6661 0.46603 0.46879 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Larval Larval Whole Organism All anatomical structures
8058 8058 ERR022485 ERX008920 ERS017423 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 434:ZF 6hpf SAMEA898399 Wellcome Sanger Institute Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 6hpf RNA from Zebrafish embryo 6hpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 4946_6.srf srf 5910514528.0 38884964.0 E MTAB 434:4946 6.srf 0:76 1:76 A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807 76 76     1741038828 1243493514 1214904056 1703863323 7214807 ERX008920 ERS017423 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.91619 0.91684 0.14961 0.15221 0.77189 0.7723 0.49092 0.49303 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-03-10 Gastrula Embryo Whole Organism All anatomical structures
8059 8059 ERR022480 ERX008923 ERS000088 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         ZF female head sample1 SAMEA708836 Wellcome Sanger Institute Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|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:ERS000088|Sample Name:ERS000088|Sex:female|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 adult female head RNA from Zebrafish adult female head 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: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head 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_5.srf srf 1622590272.0 15023984.0 E MTAB 434:2719 5.srf 0:54 1:54 A:426435544;C:373743071;G:387589492;T:432086510;N:2735655 54 54     426435544 373743071 387589492 432086510 2735655 ERX008923 ERS000088 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.94624 0.94338 0.17949 0.17965 0.66454 0.66872 0.51097 0.51377 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Head Nervous System
8060 8060 ERR022481 ERX008923 ERS000088 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         ZF female head sample1 SAMEA708836 Wellcome Sanger Institute Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|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:ERS000088|Sample Name:ERS000088|Sex:female|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 adult female head RNA from Zebrafish adult female head 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: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head 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_6.srf srf 1693460736.0 15680192.0 E MTAB 434:2719 6.srf 0:54 1:54 A:445666325;C:389360280;G:403789644;T:451529226;N:3115261 54 54     445666325 389360280 403789644 451529226 3115261 ERX008923 ERS000088 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.94579 0.94429 0.17895 0.17923 0.66864 0.67164 0.51788 0.51083 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Head Nervous System
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
9982 9982 ERR4568390 ERX4504063 ERS5050806 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep3 SAMEA7292236 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292236|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep3 p HypoTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP3_CRRA200004859-1a_HV532DSXX_L4_1.fq.gz HP3_CRRA200004859-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7117020000.0 23723400.0 E MTAB 9528:HP3 CRRA200004859 1a HV532DSXX L4 0:150 1:150 A:1864896771;C:1704008842;G:1704487221;T:1843451594;N:175572 150 150     1864896771 1704008842 1704487221 1843451594 175572 ERX4504063 ERS5050806 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94335 0.9433 0.08657 0.08625 0.72498 0.72636 0.48274 0.4859 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9983 9983 ERR4568389 ERX4504062 ERS5050805 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep2 SAMEA7292235 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292235|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep2 p HypoTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP2_CRRA200004858-1a_HV532DSXX_L4_1.fq.gz HP2_CRRA200004858-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7810736700.0 26035789.0 E MTAB 9528:HP2 CRRA200004858 1a HV532DSXX L4 0:150 1:150 A:2064202307;C:1840783570;G:1863746983;T:2041812726;N:191114 150 150     2064202307 1840783570 1863746983 2041812726 191114 ERX4504062 ERS5050805 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93642 0.93627 0.08781 0.08757 0.72841 0.72872 0.48431 0.48311 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9984 9984 ERR4568388 ERX4504061 ERS5050804 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep1 SAMEA7292234 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292234|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep1 p HypoTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP1_CRRA200004857-1a_HV532DSXX_L4_1.fq.gz HP1_CRRA200004857-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7143318600.0 23811062.0 E MTAB 9528:HP1 CRRA200004857 1a HV532DSXX L4 0:150 1:150 A:1883244963;C:1695388732;G:1697412462;T:1867096015;N:176428 150 150     1883244963 1695388732 1697412462 1867096015 176428 ERX4504061 ERS5050804 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9408 0.94186 0.08491 0.08465 0.73129 0.73099 0.47185 0.47442 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9985 9985 ERR4568387 ERX4504060 ERS5050803 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep3 SAMEA7292233 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292233|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep3 p EuTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP3_CRRA200004850-1a_HV532DSXX_L4_1.fq.gz EP3_CRRA200004850-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7860809700.0 26202699.0 E MTAB 9528:EP3 CRRA200004850 1a HV532DSXX L4 0:150 1:150 A:2068735854;C:1871645002;G:1876330645;T:2043901317;N:196882 150 150     2068735854 1871645002 1876330645 2043901317 196882 ERX4504060 ERS5050803 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93854 0.93903 0.09256 0.09314 0.74014 0.74059 0.47935 0.47779 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9986 9986 ERR4568386 ERX4504059 ERS5050802 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep2 SAMEA7292232 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292232|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep2 p EuTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP2_CRRA200004849-1a_HV532DSXX_L4_1.fq.gz EP2_CRRA200004849-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7168033200.0 23893444.0 E MTAB 9528:EP2 CRRA200004849 1a HV532DSXX L4 0:150 1:150 A:1903193161;C:1689671926;G:1689805787;T:1885183061;N:179265 150 150     1903193161 1689671926 1689805787 1885183061 179265 ERX4504059 ERS5050802 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93988 0.93957 0.08429 0.08448 0.74399 0.74375 0.4672 0.47077 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9987 9987 ERR4568385 ERX4504058 ERS5050801 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep1 SAMEA7292231 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292231|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep1 p EuTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP1_CRRA200004848-1a_HV532DSXX_L4_1.fq.gz EP1_CRRA200004848-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7993254600.0 26644182.0 E MTAB 9528:EP1 CRRA200004848 1a HV532DSXX L4 0:150 1:150 A:2055964917;C:1952736981;G:1951688671;T:2032664860;N:199171 150 150     2055964917 1952736981 1951688671 2032664860 199171 ERX4504058 ERS5050801 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94523 0.94513 0.09369 0.09348 0.74511 0.74525 0.48633 0.48842 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9988 9988 ERR4568384 ERX4504057 ERS5050800 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep3 SAMEA7292230 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292230|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep3 p HypoTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM3_CRRA200004862-1a_HV532DSXX_L4_1.fq.gz HM3_CRRA200004862-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7418093400.0 24726978.0 E MTAB 9528:HM3 CRRA200004862 1a HV532DSXX L4 0:150 1:150 A:1979368375;C:1736175227;G:1747418895;T:1954949103;N:181800 150 150     1979368375 1736175227 1747418895 1954949103 181800 ERX4504057 ERS5050800 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93389 0.93398 0.0839 0.08406 0.72147 0.72115 0.47407 0.47898 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9989 9989 ERR4568383 ERX4504056 ERS5050799 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep2 SAMEA7292229 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292229|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep2 p HypoTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM2_CRRA200004861-1a_HV532DSXX_L4_1.fq.gz HM2_CRRA200004861-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7047855300.0 23492851.0 E MTAB 9528:HM2 CRRA200004861 1a HV532DSXX L4 0:150 1:150 A:1909885369;C:1626900113;G:1623501695;T:1887391464;N:176659 150 150     1909885369 1626900113 1623501695 1887391464 176659 ERX4504056 ERS5050799 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93212 0.93173 0.08713 0.08625 0.7136 0.71411 0.47182 0.46635 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9990 9990 ERR4568382 ERX4504055 ERS5050798 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep1 SAMEA7292228 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292228|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep1 p HypoTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM1_CRRA200004860-1a_HV532DSXX_L4_1.fq.gz HM1_CRRA200004860-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7368139500.0 24560465.0 E MTAB 9528:HM1 CRRA200004860 1a HV532DSXX L4 0:150 1:150 A:1979116696;C:1681144383;G:1748755925;T:1958940264;N:182232 150 150     1979116696 1681144383 1748755925 1958940264 182232 ERX4504055 ERS5050798 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.90037 0.90035 0.07933 0.07951 0.72547 0.72512 0.46313 0.45076 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9991 9991 ERR4568381 ERX4504054 ERS5050797 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep3 SAMEA7292227 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292227|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep3 p EuTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM3_CRRA200004853-1a_HV532DSXX_L4_1.fq.gz EM3_CRRA200004853-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8203926600.0 27346422.0 E MTAB 9528:EM3 CRRA200004853 1a HV532DSXX L4 0:150 1:150 A:2145970242;C:1969430575;G:1966154582;T:2122170071;N:201130 150 150     2145970242 1969430575 1966154582 2122170071 201130 ERX4504054 ERS5050797 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9358 0.93551 0.11154 0.11215 0.73908 0.73813 0.50711 0.50991 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9992 9992 ERR4568380 ERX4504053 ERS5050796 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep2 SAMEA7292226 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292226|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep2 p EuTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM2_CRRA200004852-1a_HV532DSXX_L4_1.fq.gz EM2_CRRA200004852-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8189085300.0 27296951.0 E MTAB 9528:EM2 CRRA200004852 1a HV532DSXX L4 0:150 1:150 A:2190135788;C:1917852780;G:1910200259;T:2170694756;N:201717 150 150     2190135788 1917852780 1910200259 2170694756 201717 ERX4504053 ERS5050796 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93471 0.93387 0.0982 0.0981 0.73357 0.73401 0.47523 0.47764 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9993 9993 ERR4568379 ERX4504052 ERS5050795 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep1 SAMEA7292225 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292225|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep1 p EuTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM1_CRRA200004851-1a_HV532DSXX_L4_1.fq.gz EM1_CRRA200004851-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7099416900.0 23664723.0 E MTAB 9528:EM1 CRRA200004851 1a HV532DSXX L4 0:150 1:150 A:1906046714;C:1656677333;G:1651795527;T:1884722014;N:175312 150 150     1906046714 1656677333 1651795527 1884722014 175312 ERX4504052 ERS5050795 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93383 0.93423 0.08879 0.08881 0.73699 0.73669 0.47814 0.47895 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9994 9994 ERR4568378 ERX4504051 ERS5050794 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep3 SAMEA7292224 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292224|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep3 p HypoTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD3_CRRA200004865-1a_HV532DSXX_L4_1.fq.gz HD3_CRRA200004865-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8040672900.0 26802243.0 E MTAB 9528:HD3 CRRA200004865 1a HV532DSXX L4 0:150 1:150 A:2167099154;C:1865357004;G:1864002622;T:2144021108;N:193012 150 150     2167099154 1865357004 1864002622 2144021108 193012 ERX4504051 ERS5050794 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92854 0.92899 0.09996 0.09934 0.71902 0.71881 0.4815 0.47867 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9995 9995 ERR4568377 ERX4504050 ERS5050793 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep2 SAMEA7292223 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292223|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep2 p HypoTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD2_CRRA200004864-1a_HV532DSXX_L4_1.fq.gz HD2_CRRA200004864-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8313797700.0 27712659.0 E MTAB 9528:HD2 CRRA200004864 1a HV532DSXX L4 0:150 1:150 A:2273004120;C:1900982980;G:1898877384;T:2240725057;N:208159 150 150     2273004120 1900982980 1898877384 2240725057 208159 ERX4504050 ERS5050793 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92628 0.92613 0.09471 0.09395 0.72003 0.72054 0.47995 0.47659 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9996 9996 ERR4568376 ERX4504049 ERS5050792 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep1 SAMEA7292222 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292222|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep1 p HypoTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD1_CRRA200004863-1a_HV532DSXX_L4_1.fq.gz HD1_CRRA200004863-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7169598300.0 23898661.0 E MTAB 9528:HD1 CRRA200004863 1a HV532DSXX L4 0:150 1:150 A:1941925699;C:1655391745;G:1656382398;T:1915720427;N:178031 150 150     1941925699 1655391745 1656382398 1915720427 178031 ERX4504049 ERS5050792 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92656 0.92587 0.09244 0.09155 0.72537 0.72577 0.483 0.48459 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9997 9997 ERR4568375 ERX4504048 ERS5050791 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep3 SAMEA7292221 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292221|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep3 p EuTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED3_CRRA200004856-1a_HV532DSXX_L4_1.fq.gz ED3_CRRA200004856-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8216298900.0 27387663.0 E MTAB 9528:ED3 CRRA200004856 1a HV532DSXX L4 0:150 1:150 A:2202070307;C:1915188230;G:1918164478;T:2180672072;N:203813 150 150     2202070307 1915188230 1918164478 2180672072 203813 ERX4504048 ERS5050791 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93043 0.92995 0.07828 0.07796 0.73799 0.73912 0.46784 0.47067 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9998 9998 ERR4568374 ERX4504047 ERS5050790 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep2 SAMEA7292220 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292220|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep2 p EuTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED2_CRRA200004855-1a_HV532DSXX_L4_1.fq.gz ED2_CRRA200004855-1a_HV532DSXX_L4_2.fq.gz fastq fastq 6629601000.0 22098670.0 E MTAB 9528:ED2 CRRA200004855 1a HV532DSXX L4 0:150 1:150 A:1741036830;C:1583210201;G:1581636803;T:1723551874;N:165292 150 150     1741036830 1583210201 1581636803 1723551874 165292 ERX4504047 ERS5050790 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93472 0.93506 0.0948 0.09463 0.75235 0.75235 0.49522 0.49267 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9999 9999 ERR4568373 ERX4504046 ERS5050789 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep1 SAMEA7292219 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292219|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep1 p EuTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED1_CRRA200004854-1a_HV532DSXX_L4_1.fq.gz ED1_CRRA200004854-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7261648200.0 24205494.0 E MTAB 9528:ED1 CRRA200004854 1a HV532DSXX L4 0:150 1:150 A:1943655774;C:1694798398;G:1699834504;T:1923179081;N:180443 150 150     1943655774 1694798398 1699834504 1923179081 180443 ERX4504046 ERS5050789 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92967 0.92953 0.08728 0.08781 0.73819 0.73797 0.49368 0.49233 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
32162 32162 SRR29095835 SRX24619914 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 4 OF 4 OF 4 6 month zebrafish with proteinuria kidney 4     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_4_1.fq OF_4_2.fq fastq fastq 4377669000.0 14592230.0 OF 4 1.fq 0:150 1:150 A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987 150 150     1194166573 999239529 1001594280 1182651631 16987 SRX24619914 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32163 32163 SRR29095836 SRX24619913 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 3 OF 3 OF 3 6 month zebrafish with proteinuria kidney 3     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_3_1.fq OF_3_2.fq fastq fastq 4798165200.0 15993884.0 OF 3 1.fq 0:150 1:150 A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459 150 150     1290466714 1114007506 1115137813 1278535708 17459 SRX24619913 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32164 32164 SRR29095837 SRX24619912 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 2 OF 2 OF 2 6 month zebrafish with proteinuria kidney 2     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_2_1.fq OF_2_2.fq fastq fastq 5661202800.0 18870676.0 OF 2 1.fq 0:150 1:150 A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813 150 150     1549085619 1287400217 1288853902 1535841249 21813 SRX24619912 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32165 32165 SRR29095838 SRX24619911 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 1 OF 1 OF 1 6 month zebrafish with proteinuria kidney 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_1_1.fq OF_1_2.fq fastq fastq 5957895600.0 19859652.0 OF 1 1.fq 0:150 1:150 A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811 150 150     1627320757 1359602784 1360982917 1609967331 21811 SRX24619911 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32166 32166 SRR29095839 SRX24619910 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 4 NF 6 NF 6 6 month zebrafish kidney 4     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_6_1.fq NF_6_2.fq fastq fastq 5469504900.0 18231683.0 NF 6 1.fq 0:150 1:150 A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951 150 150     1480833386 1260945093 1261275041 1466430429 20951 SRX24619910 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32167 32167 SRR29095840 SRX24619909 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 3 NF 5 NF 5 6 month zebrafish kidney 3     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_5_1.fq NF_5_2.fq fastq fastq 6386781900.0 21289273.0 NF 5 1.fq 0:150 1:150 A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191 150 150     1743273279 1458330156 1460747658 1724406616 24191 SRX24619909 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32168 32168 SRR29095841 SRX24619908 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 2 NF 2 NF 2 6 month zebrafish kidney 2     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_2_1.fq NF_2_2.fq fastq fastq 5747851800.0 19159506.0 NF 2 1.fq 0:150 1:150 A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143 150 150     1564796254 1316015979 1317516650 1549501774 21143 SRX24619908 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32169 32169 SRR29095842 SRX24619907 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 1 NF 1 NF 1 6 month zebrafish kidney 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_1_1.fq NF_1_2.fq fastq fastq 5369089800.0 17896966.0 NF 1 1.fq 0:150 1:150 A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651 150 150     1413369042 1273865602 1277141372 1404694133 19651 SRX24619907 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
36405 36405 SRR546820 SRX180750 SRS347212 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo prim6 stage D. rerio prim6 embryo D. rerio prim6 embryo                     RNAseq D. rerio prim6 embryo RNAseq D. rerio prim6 embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_prim6_2_fix.fastq fastq 3011340704.0 19811452.0 RNAseq D. rerio prim6 embryo 0:76 1:76 A:727345664;C:767747833;G:787766862;T:725606403;N:2873942 76 76     727345664 767747833 787766862 725606403 2873942 SRX180750 SRS347212 SRA055273 University of Bergen ZEPROME consortium 2 0.94491 0.94492 0.04196 0.04323 0.76641 0.76928 0.48087 0.48787 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
36406 36406 SRR546819 SRX180749 SRS347211 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 14 somites stage D. rerio 14 somites embryo D. rerio 14 somites embryo                     RNAseq D. rerio 14 somites embryo RNAseq D. rerio 14 somites embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_14somites_2.fastq fastq 2976465520.0 19582010.0 RNAseq D. rerio 14 somites embryo 0:76 1:76 A:747831748;C:733533938;G:754151936;T:738091995;N:2855903 76 76     747831748 733533938 754151936 738091995 2855903 SRX180749 SRS347211 SRA055273 University of Bergen ZEPROME consortium 2 0.9236 0.91427 0.0861 0.08534 0.7559 0.75528 0.48428 0.47549 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Segmentation Embryo Embryo Imprecise All anatomical structures
36407 36407 SRR546818 SRX180748 SRS347209 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo dome/zfs:0000015 stage D. rerio dome/zfs:0000015 embryo D. rerio dome/zfs:0000015 embryo                     RNAseq D. rerio dome/zfs:0000015 embryo RNAseq D. rerio dome/zfs:0000015 embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_30p_dome_1.fastq fastq 2359648608.0 15524004.0 RNAseq D. rerio dome/zfs:0000015 embryo 0:76 1:76 A:588562906;C:575605218;G:603310130;T:589755481;N:2414873 76 76     588562906 575605218 603310130 589755481 2414873 SRX180748 SRS347209 SRA055273 University of Bergen ZEPROME consortium 2 0.89779 0.9222 0.04122 0.0431 0.76609 0.77112 0.49779 0.49305 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Blastula Embryo Embryo Imprecise All anatomical structures
36408 36408 SRR546817 SRX180747 SRS358988 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 2 cells stage D. rerio 2 cells embryo D. rerio 2 cells embryo                     RNAseq D. rerio 2 cells embryo RNAseq D. rerio 2 cells embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950         2799828144.0 18419922.0 RNAseq D. rerio 2 cells embryo 0:76 1:76 A:678251421;C:711410510;G:729905459;T:677312772;N:2947982 76 76     678251421 711410510 729905459 677312772 2947982 SRX180747 SRS358988 SRA055273 University of Bergen ZEPROME consortium 2 0.9498 0.94704 0.02363 0.02442 0.7988 0.80221 0.48657 0.49361 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Cleavage Embryo Embryo Imprecise All anatomical structures
36586 36586 SRR1562528 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3901027000.0 41246200.0 zebrafish data1 0:50 1:50 A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159 50 50     1065764997 896043530 867105444 1071973870 139159 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95204 0.94561 0.11416 0.11357 0.68235 0.68387 0.47537 0.47688 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36587 36587 SRR1562529 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3298508150.0 34528793.0 zebrafish data2 0:50 1:50 A:870578872;C:780299206;G:764413584;T:883098619;N:117869 50 50     870578872 780299206 764413584 883098619 117869 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.96195 0.9525 0.05344 0.0528 0.77285 0.7737 0.44453 0.43789 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36588 36588 SRR1562530 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         5033866800.0 52047991.0 zebrafish data6 0:50 1:50 A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438 50 50     1318991279 1193979085 1179037925 1341674073 184438 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.97568 0.97028 0.03448 0.03488 0.88767 0.88785 0.17745 0.18337 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36589 36589 SRR1562531 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         4394828000.0 45714707.0 zebrafish data3 0:50 1:50 A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894 50 50     1146792341 1067826128 1033443384 1146608253 157894 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.96496 0.95999 0.03952 0.03946 0.78571 0.78518 0.51359 0.49202 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36590 36590 SRR1562532 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3637203400.0 38182310.0 zebrafish data4 0:50 1:50 A:956604323;C:863740756;G:843429871;T:973297634;N:130816 50 50     956604323 863740756 843429871 973297634 130816 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95377 0.94653 0.0656 0.06507 0.72448 0.72541 0.4157 0.41707 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36591 36591 SRR1562533 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         4185424200.0 44832788.0 zebrafish data5 0:50 1:50 A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807 50 50     1143949920 959926497 921201865 1160194111 151807 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95163 0.94301 0.12015 0.11974 0.64396 0.64514 0.49698 0.49883 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
39636 39636 SRR1972985 SRX993117 SRS907736 SRP057116 PRJNA280983 Danio rerio strain:CG2 Transcriptome or Gene expression PRJNA280983 Other CG2 homozygous diploid zebrafish line.       Model organism or animal sample from Danio rerio CG2 CG2 immune related tissues   strain:CG2|dev stage:adult|sex:not determined|tissue:kidney intestine gills and spleen|BioSampleModel:Model organism or animal                 CG2 RNA seq pooled kidney intestine gills and spleen CG2 not normalized 1 A single adult CG2 zebrafish was euthanized and the kidney intestine gills and spleen were dissected and combined for RNA extraction Trizol Life Technologies. RNA was prepared for sequencing with the TruSeq RNA kit Illumina and sequenced 2 x 100 bp paired end reads on a single lane of a HiSeq2000 Illumina. Average insert size of 280 bps.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP057116     130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_2.fq.gz 130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_1.fq.gz fastq fastq 43788950600.0 218944753.0 CG2 non normalized 0:100 1:100 A:11515770713;C:10371712470;G:10317757450;T:11519383282;N:64326685 100 100     11515770713 10371712470 10317757450 11519383282 64326685 SRX993117 SRS907736 SRA258497 North Carolina State University North Carolina State University 2 0.94368 0.94427 0.05435 0.05507 0.73612 0.7376 0.53132 0.53023 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown trueseq bulk unknown unknown   United States 2015-08-05 Adult Adult Multi-tissue Multi-system
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
39824 39824 SRR2168748 SRX1153634 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT heart bulbus arteriosus transcriptome Zebrafish bulbus arteriosus Bulbus arteriosus 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <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> SRP062468     ZFBulbouse_cat_R1.fastq.gz ZFBulbouse_cat_R2.fastq.gz fastq fastq 31137941450.0 154148225.0 Zebrafish bulbus arteriosus 0:101 1:101 A:8841038901;C:6663109706;G:6831238323;T:8799856408;N:2698112 101 101     8841038901 6663109706 6831238323 8799856408 2698112 SRX1153634 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.81876 0.77794 0.54672 0.51003 0.7162 0.72752 0.54114 0.5421 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 Adult Adult Heart Cardiovascular System
39825 39825 SRR2168740 SRX1153633 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT atrium specific transcriptome Zebrafish Atrium Atrium 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <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> SRP062468     ZFAtrium_GTGAAA_L006_cat_R2.fastq.gz ZFAtrium_GTGAAA_L006_cat_R1.fastq.gz fastq fastq 28208507150.0 139646075.0 Zebrafish Atrium 0:101 1:101 A:8151737615;C:5894384726;G:6027846905;T:8129189369;N:5348535 101 101     8151737615 5894384726 6027846905 8129189369 5348535 SRX1153633 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.83701 0.79433 0.58576 0.54496 0.72486 0.73766 0.55105 0.54713 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2015-09-08 Adult Adult Heart Cardiovascular System
39826 39826 SRR2168750 SRX1153632 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish Ventricle chamber specific transcriptome Zebrafish Ventricle chamber specific transcriptome Ventricle 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <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> SRP062468     ZFVentricle_cat_R2.fastq.gz ZFVentricle_cat_R1.fastq.gz fastq fastq 30913187362.0 153035581.0 Zebrafish Ventricle chamber specific transcriptome 0:101 1:101 A:8230747947;C:7230918780;G:7381253230;T:8066864305;N:3403100 101 101     8230747947 7230918780 7381253230 8066864305 3403100 SRX1153632 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.92213 0.91404 0.22257 0.21715 0.76761 0.77193 0.54625 0.54332 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 Adult Adult Heart Cardiovascular System
39934 39934 SRR2473238 SRX1270438 SRS1078341 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.     Danio rerio embryos ectopically expressing human SPOPwt.   Danio rerio ectopic SPOPwt   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 SPOP mutation leads to genomic instability in prostate cancer Danio rerio ectopic SPOPwt 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz fastq fastq 6185345892.0 60640646.0 Danio rerio ectopic SPOPwt 0:51 1:51 A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809 51 51     1647678166 1462773970 1416249443 1657464504 1179809 SRX1270438 SRS1078341     Weill Cornell Medical College 2 0.94598 0.94553 0.09216 0.0934 0.68789 0.69065 0.46814 0.47172 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2016-02-17 Pharyngula Embryo Whole Organism All anatomical structures
39935 39935 SRR2473236 SRX1270437 SRS1078340 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.     Danio rerio ectopically expressing SPOP F133V   Danio rerio ectopic SPOP F133V   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 SPOP mutation leads to genomic instability in prostate cancer Danio rerio ectopic SPOP F133V 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz fastq fastq 6130528134.0 60103217.0 Danio rerio ectopic SPOP F133V 0:51 1:51 A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035 51 51     1630145057 1450811256 1409924927 1638457859 1189035 SRX1270437 SRS1078340     Weill Cornell Medical College 2 0.9444 0.94139 0.09809 0.0979 0.68487 0.68657 0.46751 0.47276 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2015-09-21 Pharyngula Embryo Whole Organism All anatomical structures
39936 39936 SRR2473235 SRX1270436 SRS1078339 SRP063952 PRJNA296414 SPOP mutation leads to genomic instability in prostate cancer PRJNA296414 Transcriptome Analysis Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.         Danio rerio SPOP morpholino   strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal                 Danio rerio SPOP morpholino Danio rerio SPOP morpholino 1 SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063952     Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz fastq fastq 5693947938.0 55823019.0 Danio rerio SPOP morpholino 0:51 1:51 A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641 51 51     1513477521 1350461483 1305374194 1523527099 1107641 SRX1270436 SRS1078339     Weill Cornell Medical College 2 0.94534 0.94431 0.09368 0.0945 0.68941 0.69077 0.46543 0.46749 51 51 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2016-02-17 Pharyngula Embryo Whole Organism All anatomical structures
40711 40711 SRR3420419 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz fastq fastq 2419781176.0 15919613.0 AG00719 run 1 0:76 1:76 A:738997601;C:465047900;G:477140497;T:733241052;N:5354126 76 76     738997601 465047900 477140497 733241052 5354126 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.78184 0.71182 0.66469 0.60037 0.75743 0.77518 0.53432 0.52801 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40712 40712 SRR3420420 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz fastq fastq 3074724552.0 20228451.0 AG00719 run 2 0:76 1:76 A:918671897;C:609510609;G:622542852;T:922439528;N:1559666 76 76     918671897 609510609 622542852 922439528 1559666 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76444 0.65488 0.65157 0.55185 0.75741 0.78106 0.53067 0.52622 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40713 40713 SRR3420421 SRX1660357 SRS1360318 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00719 8h 2   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00719 8h 2 AG00719 8h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz fastq fastq 2666395856.0 17542078.0 AG00719 run 3 0:76 1:76 A:787508876;C:539791618;G:549145516;T:785088342;N:4861504 76 76     787508876 539791618 549145516 785088342 4861504 SRX1660357 SRS1360318 SRA395141 Yale University|Giraldez Lab Yale University 2 0.75479 0.69465 0.63843 0.58422 0.75716 0.78423 0.53952 0.52615 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40714 40714 SRR3420388 SRX1660356 SRS1360315 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00718 8h 1   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00718 8h 1 AG00718 8h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz fastq fastq 2699903800.0 17762525.0 AG00718 run 1 0:76 1:76 A:832300161;C:503956886;G:525141498;T:832566681;N:5938574 76 76     832300161 503956886 525141498 832566681 5938574 SRX1660356 SRS1360315 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76651 0.69033 0.63937 0.56749 0.77145 0.78545 0.53429 0.53165 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40715 40715 SRR3420392 SRX1660356 SRS1360315 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00718 8h 1   strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00718 8h 1 AG00718 8h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz fastq fastq 2798947456.0 18414128.0 AG00718 run 2 0:76 1:76 A:853546590;C:536347349;G:556751964;T:851863324;N:438229 76 76     853546590 536347349 556751964 851863324 438229 SRX1660356 SRS1360315 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74665 0.63683 0.6265 0.5237 0.76134 0.7905 0.54613 0.53982 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40716 40716 SRR3420398 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz fastq fastq 1442918520.0 9492885.0 AG00717 run 1 0:76 1:76 A:442675510;C:273265985;G:284514997;T:439403136;N:3058892 76 76     442675510 273265985 284514997 439403136 3058892 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.76736 0.69048 0.60693 0.53532 0.74647 0.76138 0.51546 0.5135 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40717 40717 SRR3420402 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz fastq fastq 2524099688.0 16605919.0 AG00717 run 2 0:76 1:76 A:752163917;C:500880325;G:526291920;T:744462824;N:300702 76 76     752163917 500880325 526291920 744462824 300702 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.7274 0.651 0.57791 0.50498 0.74434 0.76329 0.51831 0.50479 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40718 40718 SRR3420405 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz fastq fastq 1320586032.0 8688066.0 AG00717 run 3 0:76 1:76 A:394339370;C:259687848;G:270914284;T:389960707;N:5683823 76 76     394339370 259687848 270914284 389960707 5683823 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.72219 0.6734 0.55665 0.5122 0.75371 0.76323 0.5098 0.50658 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40719 40719 SRR3420409 SRX1660355 SRS1360316 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00717 6h 2   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal                 AG00717 6h 2 AG00717 6h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz fastq fastq 1778143272.0 11698311.0 AG00717 run 4 0:76 1:76 A:531893644;C:351009327;G:366187476;T:528937189;N:115636 76 76     531893644 351009327 366187476 528937189 115636 SRX1660355 SRS1360316 SRA395141 Yale University|Giraldez Lab Yale University 2 0.72027 0.6573 0.57252 0.50814 0.74913 0.77479 0.51537 0.50066 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40720 40720 SRR3420315 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz fastq fastq 1837024424.0 12085687.0 AG00716 run 1 0:76 1:76 A:571581150;C:339887376;G:357200726;T:564453542;N:3901630 76 76     571581150 339887376 357200726 564453542 3901630 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.77818 0.69777 0.64211 0.56481 0.75503 0.76926 0.50584 0.51507 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40721 40721 SRR3420319 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz fastq fastq 2763994600.0 18184175.0 AG00716 run 2 0:76 1:76 A:841712204;C:530711238;G:562110067;T:828853061;N:608030 76 76     841712204 530711238 562110067 828853061 608030 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74716 0.66787 0.61425 0.53764 0.7475 0.76518 0.50855 0.51311 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40722 40722 SRR3420323 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz fastq fastq 1055704904.0 6945427.0 AG00716 run 3 0:76 1:76 A:323142351;C:199674907;G:210508599;T:317806564;N:4572483 76 76     323142351 199674907 210508599 317806564 4572483 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.73664 0.68701 0.59387 0.5447 0.76179 0.76132 0.51299 0.51552 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Gastrula Embryo Whole Organism All anatomical structures
40723 40723 SRR3420327 SRX1660354 SRS1360300 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00716 6h 1   strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal                 AG00716 6h 1 AG00716 6h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz fastq fastq 2526928408.0 16624529.0 AG00716 run 4 0:76 1:76 A:771333886;C:482964782;G:508687112;T:763609426;N:333202 76 76     771333886 482964782 508687112 763609426 333202 SRX1660354 SRS1360300 SRA395141 Yale University|Giraldez Lab Yale University 2 0.74535 0.66478 0.61452 0.53584 0.75826 0.77329 0.51139 0.51539 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-04-22 Gastrula Embryo Whole Organism All anatomical structures
40724 40724 SRR3420333 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz fastq fastq 2314408088.0 15226369.0 AG00715 run 1 0:76 1:76 A:652783335;C:485705748;G:507451689;T:663544778;N:4922538 76 76     652783335 485705748 507451689 663544778 4922538 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.59859 0.55293 0.24175 0.21943 0.78384 0.79174 0.52173 0.52111 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40725 40725 SRR3420337 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz fastq fastq 2461668424.0 16195187.0 AG00715 run 2 0:76 1:76 A:653884256;C:562168304;G:597853484;T:647470498;N:291882 76 76     653884256 562168304 597853484 647470498 291882 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.5374 0.51402 0.2167 0.19427 0.78575 0.7934 0.52714 0.53043 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40726 40726 SRR3420341 SRX1660350 SRS1360304 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00715 4h 2   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal                 AG00715 4h 2 AG00715 4h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz fastq fastq 3692351624.0 24291787.0 AG00715 run 3 0:76 1:76 A:984283909;C:835828915;G:881112020;T:975490829;N:15635951 76 76     984283909 835828915 881112020 975490829 15635951 SRX1660350 SRS1360304 SRA395141 Yale University|Giraldez Lab Yale University 2 0.54752 0.52404 0.18037 0.16908 0.79358 0.7961 0.50982 0.50975 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40727 40727 SRR3420346 SRX1660346 SRS1360308 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00714 4h 1   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal                 AG00714 4h 1 AG00714 4h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz fastq fastq 2377192296.0 15639423.0 AG00714 run 1 0:76 1:76 A:694380135;C:473427723;G:496920379;T:707435115;N:5028944 76 76     694380135 473427723 496920379 707435115 5028944 SRX1660346 SRS1360308 SRA395141 Yale University|Giraldez Lab Yale University 2 0.69444 0.63521 0.40011 0.36148 0.76252 0.77116 0.50751 0.5108 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40728 40728 SRR3420349 SRX1660346 SRS1360308 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00714 4h 1   strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal                 AG00714 4h 1 AG00714 4h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz fastq fastq 1841902256.0 12117778.0 AG00714 run 2 0:76 1:76 A:517451432;C:392444197;G:415696773;T:508506741;N:7803113 76 76     517451432 392444197 415696773 508506741 7803113 SRX1660346 SRS1360308 SRA395141 Yale University|Giraldez Lab Yale University 2 0.63625 0.60304 0.3341 0.31189 0.77224 0.77703 0.50754 0.51039 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40729 40729 SRR3420359 SRX1660342 SRS1360312 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00713 3h 2   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal                 AG00713 3h 2 AG00713 3h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz fastq fastq 2674764976.0 17597138.0 AG00713 run 1 0:76 1:76 A:738399424;C:560443522;G:578733188;T:791450319;N:5738523 76 76     738399424 560443522 578733188 791450319 5738523 SRX1660342 SRS1360312 SRA395141 Yale University|Giraldez Lab Yale University 2 0.63595 0.60509 0.17579 0.17695 0.79066 0.79815 0.49657 0.4916 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40730 40730 SRR3420362 SRX1660342 SRS1360312 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00713 3h 2   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal                 AG00713 3h 2 AG00713 3h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz fastq fastq 2463895376.0 16209838.0 AG00713 run 2 0:76 1:76 A:661360403;C:556078326;G:581335469;T:654625128;N:10496050 76 76     661360403 556078326 581335469 654625128 10496050 SRX1660342 SRS1360312 SRA395141 Yale University|Giraldez Lab Yale University 2 0.58767 0.56878 0.14864 0.14485 0.79476 0.79898 0.49508 0.49769 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40731 40731 SRR3420369 SRX1660341 SRS1360313 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00712 3h 1   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal                 AG00712 3h 1 AG00712 3h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz fastq fastq 1354427464.0 8910707.0 AG00712 run 1 0:76 1:76 A:382647488;C:281900295;G:291990859;T:395032379;N:2856443 76 76     382647488 281900295 291990859 395032379 2856443 SRX1660341 SRS1360313 SRA395141 Yale University|Giraldez Lab Yale University 2 0.64156 0.60052 0.23835 0.22296 0.78025 0.78717 0.49813 0.49898 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40732 40732 SRR3420375 SRX1660341 SRS1360313 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00712 3h 1   strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal                 AG00712 3h 1 AG00712 3h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz fastq fastq 2335782480.0 15366990.0 AG00712 run 2 0:76 1:76 A:638971995;C:517112038;G:538588809;T:640731763;N:377875 76 76     638971995 517112038 538588809 640731763 377875 SRX1660341 SRS1360313 SRA395141 Yale University|Giraldez Lab Yale University 2 0.60525 0.56571 0.24772 0.21069 0.77043 0.78543 0.50862 0.50386 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40733 40733 SRR3420379 SRX1660340 SRS1360314 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00711 2.5h 2   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00711 2.5h 2 AG00711 2.5h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz fastq fastq 2343343264.0 15416732.0 AG00711 run 1 0:76 1:76 A:645206414;C:505367235;G:523792864;T:663977432;N:4999319 76 76     645206414 505367235 523792864 663977432 4999319 SRX1660340 SRS1360314 SRA395141 Yale University|Giraldez Lab Yale University 2 0.59395 0.56211 0.10259 0.10243 0.80598 0.80911 0.51352 0.53772 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40734 40734 SRR3420383 SRX1660340 SRS1360314 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00711 2.5h 2   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal                 AG00711 2.5h 2 AG00711 2.5h 2 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz fastq fastq 2668460776.0 17555663.0 AG00711 run 2 0:76 1:76 A:709820753;C:602900273;G:626554840;T:717828006;N:11356904 76 76     709820753 602900273 626554840 717828006 11356904 SRX1660340 SRS1360314 SRA395141 Yale University|Giraldez Lab Yale University 2 0.56281 0.54232 0.09217 0.09047 0.80657 0.81018 0.50757 0.52507 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40735 40735 SRR3420304 SRX1660339 SRS1360299 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00710 2.5h 1   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00710 2.5h 1 AG00710 2.5h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz fastq fastq 2705199784.0 17797367.0 AG00710 run 1 0:76 1:76 A:737065338;C:573787464;G:595216660;T:793361986;N:5768336 76 76     737065338 573787464 595216660 793361986 5768336 SRX1660339 SRS1360299 SRA395141 Yale University|Giraldez Lab Yale University 2 0.60426 0.58122 0.08196 0.09224 0.80578 0.8075 0.50121 0.50121 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
40736 40736 SRR3420308 SRX1660339 SRS1360299 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG00710 2.5h 1   strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal                 AG00710 2.5h 1 AG00710 2.5h 1 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz fastq fastq 2275540168.0 14970659.0 AG00710 run 2 0:76 1:76 A:614429428;C:505827101;G:528906356;T:616697803;N:9679480 76 76     614429428 505827101 528906356 616697803 9679480 SRX1660339 SRS1360299 SRA395141 Yale University|Giraldez Lab Yale University 2 0.57792 0.56382 0.07268 0.07246 0.80261 0.80612 0.49743 0.50296 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Blastula Embryo Whole Organism All anatomical structures
41381 41381 SRR4375307 SRX2226800 SRS1732678 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B1 resa AG01072   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B1 AG01072.1 AG01072.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz fastq fastq 756436968.0 4976559.0 AG01072.1 R2.fastq.gz 0:76 1:76 A:277813562;C:101592220;G:103435859;T:273576694;N:18633 76 76     277813562 101592220 103435859 273576694 18633 SRX2226800 SRS1732678 SRA482696 Yale University|Genetics Yale University 2 0.00777 0.00795 0.00043 0.00056 0.99344 0.99389 0.43869 0.43095 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-10-06 Undetermined Embryo Embryo Imprecise All anatomical structures
41382 41382 SRR4375306 SRX2226799 SRS1732692 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B3 resa AG01070   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B3 AG01070.1 AG01070.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz fastq fastq 601712368.0 3958634.0 AG01070.1 R2.fastq.gz 0:76 1:76 A:188474921;C:113643606;G:114382568;T:185195364;N:15909 76 76     188474921 113643606 114382568 185195364 15909 SRX2226799 SRS1732692 SRA482696 Yale University|Genetics Yale University 2 0.84037 0.84016 0.03493 0.03544 0.97303 0.97252 0.46337 0.47093 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41383 41383 SRR4375305 SRX2226798 SRS1732691 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B2 resa AG01069   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B2 AG01069.1 AG01069.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz fastq fastq 1344477848.0 8845249.0 AG01069.1 R1.fastq.gz 0:76 1:76 A:418545593;C:256422789;G:257715519;T:411760293;N:33654 76 76     418545593 256422789 257715519 411760293 33654 SRX2226798 SRS1732691 SRA482696 Yale University|Genetics Yale University 2 0.84542 0.84566 0.03642 0.03588 0.97084 0.97197 0.4739 0.48121 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41384 41384 SRR4375304 SRX2226797 SRS1732690 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B1 resa AG01068   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B1 AG01068.1 AG01068.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz fastq fastq 896200056.0 5896053.0 AG01068.1 R2.fastq.gz 0:76 1:76 A:278768309;C:171161843;G:172303088;T:273944252;N:22564 76 76     278768309 171161843 172303088 273944252 22564 SRX2226797 SRS1732690 SRA482696 Yale University|Genetics Yale University 2 0.83862 0.83897 0.0351 0.03585 0.97183 0.97204 0.47364 0.47138 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41385 41385 SRR4375303 SRX2226796 SRS1732689 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B3 resa AG01067   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B3 AG01067.1 AG01067.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz fastq fastq 1799778192.0 11840646.0 AG01067.1 R1.fastq.gz 0:76 1:76 A:561491448;C:342221462;G:343998479;T:552022535;N:44268 76 76     561491448 342221462 343998479 552022535 44268 SRX2226796 SRS1732689 SRA482696 Yale University|Genetics Yale University 2 0.84432 0.84397 0.03554 0.03522 0.97224 0.9725 0.46732 0.46922 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41386 41386 SRR4375302 SRX2226795 SRS1732688 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B2 resa AG01066   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B2 AG01066.1 AG01066.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz fastq fastq 1313436864.0 8641032.0 AG01066.1 R2.fastq.gz 0:76 1:76 A:409666264;C:249755645;G:251028600;T:402953610;N:32745 76 76     409666264 249755645 251028600 402953610 32745 SRX2226795 SRS1732688 SRA482696 Yale University|Genetics Yale University 2 0.84584 0.84611 0.0349 0.03543 0.97189 0.97175 0.47547 0.48555 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41387 41387 SRR4375301 SRX2226794 SRS1732687 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B1 resa AG01065   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B1 AG01065.1 AG01065.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz fastq fastq 1442385152.0 9489376.0 AG01065.1 R2.fastq.gz 0:76 1:76 A:449362282;C:274879749;G:276626223;T:441480173;N:36725 76 76     449362282 274879749 276626223 441480173 36725 SRX2226794 SRS1732687 SRA482696 Yale University|Genetics Yale University 2 0.8417 0.84205 0.03519 0.03559 0.97193 0.97179 0.47697 0.46118 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41388 41388 SRR4375300 SRX2226793 SRS1732685 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA CLIP Ago2 RESA CLIP Ago2 input resa clip ago2 AG01631   strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:5% input before pulldown|condition:input|BioSampleModel:Model organism or animal                 RESA CLIP Ago2 RESA CLIP Ago2 input AG01631.1 AG01631.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz fastq fastq 9864834960.0 64900230.0 AG01631.1 R2.fastq.gz 0:76 1:76 A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520 76 76     2990534603 1958949912 1963153108 2951932817 264520 SRX2226793 SRS1732685 SRA482696 Yale University|Genetics Yale University 2 0.83121 0.85078 0.03505 0.0364 0.97171 0.97019 0.46925 0.47246 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Blastula Embryo Embryo Imprecise All anatomical structures
41389 41389 SRR4375299 SRX2226779 SRS1732684 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA CLIP Ago2 RESA CLIP Ago2 IP resa clip ago2 AG01630   strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:flag bead pulldown post crosslinking|condition:Ago2 IP|BioSampleModel:Model organism or animal                 RESA CLIP Ago2 RESA CLIP Ago2 IP AG01630.1 AG01630.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz fastq fastq 9348207632.0 61501366.0 AG01630.1 R1.fastq.gz 0:76 1:76 A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848 76 76     2819572908 1871537719 1881735941 2775115216 245848 SRX2226779 SRS1732684 SRA482696 Yale University|Genetics Yale University 2 0.80207 0.78648 0.02992 0.02839 0.97885 0.97871 0.49297 0.49107 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Blastula Embryo Embryo Imprecise All anatomical structures
41390 41390 SRR4375197 SRX2226727 SRS1732683 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B3 resa AG01086   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B3 AG01086.2 AG01086.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz fastq fastq 714848400.0 4702950.0 AG01086.2 R2.fastq.gz 0:76 1:76 A:261928616;C:96586565;G:97768464;T:258351392;N:213363 76 76     261928616 96586565 97768464 258351392 213363 SRX2226727 SRS1732683 SRA482696 Yale University|Genetics Yale University 2 0.00715 0.00733 0.00046 0.00044 0.99417 0.99435 0.46775 0.42207 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41391 41391 SRR4375176 SRX2226710 SRS1732686 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 64c pA r3 B2 resa AG01061   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 64c pA r3 B2 AG01061.1 AG01061.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz fastq fastq 724448416.0 4766108.0 AG01061.1 R2.fastq.gz 0:76 1:76 A:224701149;C:138989041;G:139762199;T:220977796;N:18231 76 76     224701149 138989041 139762199 220977796 18231 SRX2226710 SRS1732686 SRA482696 Yale University|Genetics Yale University 2 0.84913 0.84756 0.03557 0.03568 0.97153 0.97116 0.47281 0.46157 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-10-06 Cleavage Embryo Embryo Imprecise All anatomical structures
41392 41392 SRR4375175 SRX2226709 SRS1732683 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B3 resa AG01086   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B3 AG01086.1 AG01086.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz fastq fastq 411922128.0 2710014.0 AG01086.1 R1.fastq.gz 0:76 1:76 A:150812258;C:55795177;G:56809368;T:148495332;N:9993 76 76     150812258 55795177 56809368 148495332 9993 SRX2226709 SRS1732683 SRA482696 Yale University|Genetics Yale University 2 0.00798 0.00746 0.00062 0.00055 0.99385 0.99399 0.44328 0.47308 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41393 41393 SRR4375146 SRX2226694 SRS1732682 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B2 resa AG01085   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B2 AG01085.2 AG01085.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz fastq fastq 700337720.0 4607485.0 AG01085.2 R1.fastq.gz 0:76 1:76 A:256568404;C:94627005;G:95783677;T:253149693;N:208941 76 76     256568404 94627005 95783677 253149693 208941 SRX2226694 SRS1732682 SRA482696 Yale University|Genetics Yale University 2 0.00733 0.00726 0.00055 0.00048 0.99413 0.99393 0.46893 0.45795 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41394 41394 SRR4375102 SRX2226674 SRS1732682 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B2 resa AG01085   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B2 AG01085.1 AG01085.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz fastq fastq 409587712.0 2694656.0 AG01085.1 R1.fastq.gz 0:76 1:76 A:149931448;C:55481183;G:56493706;T:147671446;N:9929 76 76     149931448 55481183 56493706 147671446 9929 SRX2226674 SRS1732682 SRA482696 Yale University|Genetics Yale University 2 0.0079 0.0078 0.00056 0.0005 0.99366 0.99385 0.42647 0.47214 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41395 41395 SRR4375101 SRX2226673 SRS1732681 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B1 resa AG01084   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B1 AG01084.2 AG01084.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz fastq fastq 396825488.0 2610694.0 AG01084.2 R1.fastq.gz 0:76 1:76 A:145317384;C:53679748;G:54375412;T:143331621;N:121323 76 76     145317384 53679748 54375412 143331621 121323 SRX2226673 SRS1732681 SRA482696 Yale University|Genetics Yale University 2 0.0071 0.00673 0.00044 0.00042 0.99417 0.99419 0.44659 0.45357 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41396 41396 SRR4375100 SRX2226672 SRS1732681 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B1 resa AG01084   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B1 AG01084.1 AG01084.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz fastq fastq 236514888.0 1556019.0 AG01084.1 R1.fastq.gz 0:76 1:76 A:86560104;C:32062698;G:32664624;T:85221432;N:6030 76 76     86560104 32062698 32664624 85221432 6030 SRX2226672 SRS1732681 SRA482696 Yale University|Genetics Yale University 2 0.00756 0.00706 0.00061 0.00064 0.99405 0.99419 0.47228 0.48736 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41397 41397 SRR4375099 SRX2226671 SRS1732680 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B3 resa AG01074   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B3 AG01074.2 AG01074.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz fastq fastq 1411678568.0 9287359.0 AG01074.2 R1.fastq.gz 0:76 1:76 A:518452828;C:189515599;G:191777773;T:511511925;N:420443 76 76     518452828 189515599 191777773 511511925 420443 SRX2226671 SRS1732680 SRA482696 Yale University|Genetics Yale University 2 0.00745 0.00729 0.00047 0.00045 0.99405 0.99411 0.43814 0.47981 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures

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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");;