rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
8055,ERR022484,ERX008924,ERS017427,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 2cells,SAMEA898400,Wellcome Sanger Institute,Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2cells,RNA from Zebrafish embryo 2cells,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_5.srf,srf,3947547008.0,25970704.0,E MTAB 434:4946 5.srf,0:76 1:76,A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500,76,76,,,1069302461,914233601,902631356,1055986090,5393500,ERX008924,ERS017427,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.93356,0.93346,0.03988,0.04022,0.79135,0.79198,0.48864,0.48464,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
8056,ERR022486,ERX008922,ERS012705,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 1 dpf,RNA from Zebrafish embryo 1 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_3.srf,srf,4788693120.0,31504560.0,E MTAB 434:5141 3.srf,0:76 1:76,A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244,76,76,,,1329328273,1071568772,1063807333,1316891498,7097244,ERX008922,ERS012705,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95867,0.95691,0.14543,0.14805,0.69753,0.70078,0.46273,0.47662,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
8057,ERR022488,ERX008921,ERS012706,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 3 dpf 2,SAMEA898404,Wellcome Sanger Institute,Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 3 dpf,RNA from Zebrafish embryo 3 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_6.srf,srf,3787933176.0,24920613.0,E MTAB 434:5141 6.srf,0:76 1:76,A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818,76,76,,,1051092006,842721213,838644314,1048667825,6807818,ERX008921,ERS012706,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95952,0.95914,0.16277,0.16553,0.66352,0.6661,0.46603,0.46879,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
8058,ERR022485,ERX008920,ERS017423,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 6hpf,SAMEA898399,Wellcome Sanger Institute,Age:6 hours|Alias:E MTAB 434:ZF 6hpf|Broker name:ArrayExpress|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017423|Sample Name:ERS017423|Sex:mixed|StrainOrLine:Tupfel long fin|Title:ZF 6hpf,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 6hpf,RNA from Zebrafish embryo 6hpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:6 h|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_6.srf,srf,5910514528.0,38884964.0,E MTAB 434:4946 6.srf,0:76 1:76,A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807,76,76,,,1741038828,1243493514,1214904056,1703863323,7214807,ERX008920,ERS017423,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.91619,0.91684,0.14961,0.15221,0.77189,0.7723,0.49092,0.49303,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Gastrula,Embryo,Whole Organism,All anatomical structures
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,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,ERR022482,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_7.srf,srf,1764668160.0,16339520.0,E MTAB 434:2719 7.srf,0:54 1:54,A:470580161;C:399075336;G:417290042;T:474450367;N:3272254,54,54,,,470580161,399075336,417290042,474450367,3272254,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.9454,0.94288,0.20211,0.2029,0.66856,0.67207,0.4856,0.48119,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8062,ERR022483,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_8.srf,srf,1678321188.0,15540011.0,E MTAB 434:2719 8.srf,0:54 1:54,A:446988405;C:380486018;G:396533911;T:451117596;N:3195258,54,54,,,446988405,380486018,396533911,451117596,3195258,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94565,0.94277,0.19929,0.19877,0.66584,0.67014,0.47973,0.46826,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8063,ERR022487,ERX008918,ERS012707,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 2 dpf 2,SAMEA898403,Wellcome Sanger Institute,Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2 dpf,RNA from Zebrafish embryo 2 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:2 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_5.srf,srf,4321796696.0,28432873.0,E MTAB 434:5141 5.srf,0:76 1:76,A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424,76,76,,,1185782721,976784015,973264244,1178952292,7013424,ERX008918,ERS012707,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96001,0.95851,0.15373,0.15636,0.69051,0.69576,0.47409,0.47525,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Hatching,Embryo,Whole Organism,All anatomical structures
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
10056,ERR4691987,ERX4613068,ERS5216074,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457891,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,MCU_2.fastq.gz,fastq,1291626898.0,35072619.0,ena RUN UCLA 16 10 2020 22:30:43:819 4,0:36.83 1:0,A:364596432;C:305716590;G:295397140;T:324498501;N:1418235,36,0,,,364596432,305716590,295397140,324498501,1418235,ERX4613068,ERS5216074,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.93311,,0.08182,,0.75852,,0.54813,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10057,ERR4691986,ERX4613067,ERS5216073,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457890,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,MCU_1.fastq.gz,fastq,1236033124.0,33559740.0,ena RUN UCLA 16 10 2020 22:30:43:819 3,0:36.83 1:0,A:348518065;C:293502111;G:279181983;T:313506799;N:1324166,36,0,,,348518065,293502111,279181983,313506799,1324166,ERX4613067,ERS5216073,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92798,,0.07907,,0.7697,,0.5488,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10058,ERR4691985,ERX4613066,ERS5216072,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457889,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,WT_2.fastq.gz,fastq,1180831209.0,32069533.0,ena RUN UCLA 16 10 2020 22:30:43:819 2,0:36.82 1:0,A:328604642;C:281065336;G:278743466;T:291039015;N:1378750,36,0,,,328604642,281065336,278743466,291039015,1378750,ERX4613066,ERS5216072,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92319,,0.08946,,0.75706,,0.49996,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10059,ERR4691984,ERX4613065,ERS5216071,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457888,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,WT_1.fastq.gz,fastq,1428414407.0,38793098.0,ena RUN UCLA 16 10 2020 22:30:43:819 1,0:36.82 1:0,A:398925739;C:338731211;G:333527196;T:355553981;N:1676280,36,0,,,398925739,338731211,333527196,355553981,1676280,ERX4613065,ERS5216071,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92407,,0.08758,,0.75726,,0.4969,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
10213,ERR6511329,ERX6138165,ERS7264188,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep1,SAMEA9541418,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,cDNA786327,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep1.tar.gz,nanopore,1745399583.0,1644167.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,0:1061.57,A:449704009;C:421915878;G:378879857;T:494899839;N:0,1061,,,,449704009,421915878,378879857,494899839,0,ERX6138165,ERS7264188,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.01112,,0.0,,0.99997,,1.0,,546,,T,,long read,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
10215,ERR6511330,ERX6138166,ERS7264189,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep2,SAMEA9541419,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,cDNA123791,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep2.tar.gz,nanopore,2038398139.0,1955617.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,0:1042.33,A:518369802;C:477535545;G:441294056;T:601198736;N:0,1042,,,,518369802,477535545,441294056,601198736,0,ERX6138166,ERS7264189,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
25302,SRR25793493,SRX21515745,SRS18742910,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,miR 144,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,CD 144 1,CD 144 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq,fastq fastq,12899093774.0,108395746.0,CD 144 1 S3 R1.fastq,0:28 1:91,A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616,28,91,,,3225260764,3211986177,3151471558,3308055659,2319616,SRX21515745,SRS18742910,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00483,0.97382,0.00157,0.05913,0.99439,0.86815,0.46634,0.45907,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25303,SRR25793494,SRX21515744,SRS18742909,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT Wild type Danio rerio,WT,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT Wild type Danio rerio,CD wt 1,CD wt 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq,fastq fastq,12715533299.0,106853221.0,CD wt 1 S2 R1.fastq,0:28 1:91,A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346,28,91,,,3324705878,3042843364,3105568183,3240105528,2310346,SRX21515744,SRS18742909,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00593,0.93177,0.00191,0.09596,0.99257,0.84394,0.42447,0.4869,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
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,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,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,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,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,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,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,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,SRR546820,SRX180750,SRS347212,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo prim6 stage,D. rerio prim6 embryo,D. rerio prim6 embryo,,,,,,,,,,,RNAseq   D. rerio prim6 embryo,RNAseq   D. rerio prim6 embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_prim6_2_fix.fastq,fastq,3011340704.0,19811452.0,RNAseq   D. rerio prim6 embryo,0:76 1:76,A:727345664;C:767747833;G:787766862;T:725606403;N:2873942,76,76,,,727345664,767747833,787766862,725606403,2873942,SRX180750,SRS347212,SRA055273,University of Bergen,ZEPROME consortium,2,0.94491,0.94492,0.04196,0.04323,0.76641,0.76928,0.48087,0.48787,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36406,SRR546819,SRX180749,SRS347211,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 14 somites stage,D. rerio 14 somites embryo,D. rerio 14 somites embryo,,,,,,,,,,,RNAseq   D. rerio 14 somites embryo,RNAseq   D. rerio 14 somites embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_14somites_2.fastq,fastq,2976465520.0,19582010.0,RNAseq   D. rerio 14 somites embryo,0:76 1:76,A:747831748;C:733533938;G:754151936;T:738091995;N:2855903,76,76,,,747831748,733533938,754151936,738091995,2855903,SRX180749,SRS347211,SRA055273,University of Bergen,ZEPROME consortium,2,0.9236,0.91427,0.0861,0.08534,0.7559,0.75528,0.48428,0.47549,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
36407,SRR546818,SRX180748,SRS347209,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage,D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,,,,,,,,,,,RNAseq   D. rerio dome/zfs:0000015 embryo,RNAseq   D. rerio dome/zfs:0000015 embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,RNAseq_30p_dome_1.fastq,fastq,2359648608.0,15524004.0,RNAseq   D. rerio dome/zfs:0000015 embryo,0:76 1:76,A:588562906;C:575605218;G:603310130;T:589755481;N:2414873,76,76,,,588562906,575605218,603310130,589755481,2414873,SRX180748,SRS347209,SRA055273,University of Bergen,ZEPROME consortium,2,0.89779,0.9222,0.04122,0.0431,0.76609,0.77112,0.49779,0.49305,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36408,SRR546817,SRX180747,SRS358988,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 2 cells stage,D. rerio 2 cells embryo,D. rerio 2 cells embryo,,,,,,,,,,,RNAseq   D. rerio 2 cells embryo,RNAseq   D. rerio 2 cells embryo,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,2799828144.0,18419922.0,RNAseq   D. rerio 2 cells embryo,0:76 1:76,A:678251421;C:711410510;G:729905459;T:677312772;N:2947982,76,76,,,678251421,711410510,729905459,677312772,2947982,SRX180747,SRS358988,SRA055273,University of Bergen,ZEPROME consortium,2,0.9498,0.94704,0.02363,0.02442,0.7988,0.80221,0.48657,0.49361,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,Unknown,2015-07-22,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
36581,SRR594769,SRX195432,SRS369361,SRP016134,PRJNA177654,Danio rerio Transcriptome or Gene expression,PRJNA177654,Other,We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.,,,1,Test,GFP Negative 1,,,,,,,,,,,Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development,Embryos,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016134,,,,,2525199228.0,65962848.0,GFP Positive,0:38.28,A:665802914;C:594493287;G:612298433;T:652078696;N:525898,38,,,,665802914,594493287,612298433,652078696,525898,SRX195432,SRS369361,,,University of Cambridge,1,0.89062,,0.09595,,0.74059,,0.47506,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United Kingdom,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36582,SRR594771,SRX195432,SRS369361,SRP016134,PRJNA177654,Danio rerio Transcriptome or Gene expression,PRJNA177654,Other,We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.,,,1,Test,GFP Negative 1,,,,,,,,,,,Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development,Embryos,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016134,,,gfp_negative_replicate_1_sequence.txt.gz,fastq,2549682148.0,66546682.0,GFP Negative,0:38.31,A:686329592;C:587342682;G:601330559;T:674194074;N:485241,38,,,,686329592,587342682,601330559,674194074,485241,SRX195432,SRS369361,,,University of Cambridge,1,0.90413,,0.13272,,0.71342,,0.48186,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United Kingdom,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
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,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,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,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,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,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
36739,SRR867022,SRX286270,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat,Danio rerio boot,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP022549,,,s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta,SOLiD_native SOLiD_native,9801985250.0,196039705.0,Zebrafish DV patterning Boot,0:50,0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939,50,,,,,,,,,SRX286270,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.59289,,0.09435,,0.92669,,0.7658,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36740,SRR867023,SRX286271,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  ICH,Danio rerio ICH,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP022549,,,s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual,SOLiD_native SOLiD_native,10810535400.0,216210708.0,Zebrafish DV patterning ICH,0:50,0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417,50,,,,,,,,,SRX286271,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.42474,,0.06136,,0.93434,,0.75757,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36761,SRR10295266,SRX7008094,SRS431105,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT 2hpf Total mRNA,GSM1152440,,source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,,,,,,,,,WT 64c R0,AGR000324,AGR000324,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,AGR000324_R1.fastq.gz,fastq,781504124.0,10282949.0,AGR000324 R1.fastq.gz,0:76,A:151879560;C:240178928;G:220957551;T:168456166;N:31919,76,,,,151879560,240178928,220957551,168456166,31919,SRX7008094,SRS431105,SRA980383,Yale_Giraldez|Genetics,"Giraldez Lab, Genetics, Yale University",1,0.88875,,0.14141,,0.796,,0.72154,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-10-16,Cleavage,Embryo,Whole Organism,All anatomical structures
37921,SRR1554495,SRX685396,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_3.fq.gz,fastq,1225610154.0,12134754.0,Ovary2 Run3,0:101,A:347141358;C:303255805;G:280185540;T:294456010;N:571441,101,,,,347141358,303255805,280185540,294456010,571441,SRX685396,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37922,SRR1554492,SRX685395,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_3.fq.gz,fastq,1192024422.0,11802222.0,Testis2 Run3,0:101,A:373380865;C:276125943;G:251033102;T:290931637;N:552875,101,,,,373380865,276125943,251033102,290931637,552875,SRX685395,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,1e-05,,0.99997,,0.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37923,SRR1554489,SRX685394,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_3.fq.gz,fastq,1302765670.0,12898670.0,Heart2 Run3,0:101,A:397689061;C:312745449;G:268626802;T:323141419;N:562939,101,,,,397689061,312745449,268626802,323141419,562939,SRX685394,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37924,SRR1554486,SRX685392,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_3.fq.gz,fastq,1211892536.0,11998936.0,Brain2 Run3,0:101,A:374228993;C:286134640;G:253944548;T:297038575;N:545780,101,,,,374228993,286134640,253944548,297038575,545780,SRX685392,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37925,SRR1554483,SRX685391,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_3.fq.gz,fastq,347516154.0,3440754.0,Ovary1 Run3,0:101,A:107805981;C:80183725;G:73617313;T:85763181;N:145954,101,,,,107805981,80183725,73617313,85763181,145954,SRX685391,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,4e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37926,SRR1554480,SRX685390,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_3.fq.gz,fastq,1184228636.0,11725036.0,Testis1 Run3,0:101,A:340636900;C:278505979;G:259975802;T:304564724;N:545231,101,,,,340636900,278505979,259975802,304564724,545231,SRX685390,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,1e-05,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37927,SRR1554477,SRX685389,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_3.fq.gz,fastq,1561371524.0,15459124.0,Heart1 Run3,0:101,A:454757966;C:391143691;G:334715236;T:380114024;N:640607,101,,,,454757966,391143691,334715236,380114024,640607,SRX685389,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37928,SRR1554474,SRX685388,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_3.fq.gz,fastq,1192445794.0,11806394.0,Brain1 Run3,0:101,A:369786121;C:268557682;G:265557417;T:288006805;N:537769,101,,,,369786121,268557682,265557417,288006805,537769,SRX685388,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37929,SRR1554493,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_1.fq.gz,fastq,476104278.0,9335378.0,Ovary2 Run1,0:51,A:111060704;C:120863975;G:129849761;T:114224677;N:105161,51,,,,111060704,120863975,129849761,114224677,105161,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00027,,8e-05,,0.99945,,0.8125,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37930,SRR1554494,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_2.fq.gz,fastq,561956352.0,11018752.0,Ovary2 Run2,0:51,A:129925815;C:148479658;G:148478706;T:132824290;N:2247883,51,,,,129925815,148479658,148478706,132824290,2247883,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,0.0001,,0.99967,,0.6875,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37931,SRR1554490,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_1.fq.gz,fastq,586152231.0,11493181.0,Testis2 Run1,0:51,A:145360493;C:148943988;G:151402108;T:140286245;N:159397,51,,,,145360493,148943988,151402108,140286245,159397,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37932,SRR1554491,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_2.fq.gz,fastq,697016337.0,13666987.0,Testis2 Run2,0:51,A:172082858;C:184634425;G:173370430;T:163527914;N:3400710,51,,,,172082858,184634425,173370430,163527914,3400710,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37933,SRR1554487,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_1.fq.gz,fastq,767836212.0,15055612.0,Heart2 Run1,0:51,A:192620363;C:202013249;G:191038597;T:181862075;N:301928,51,,,,192620363,202013249,191038597,181862075,301928,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,3e-05,,0.99995,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37934,SRR1554488,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_2.fq.gz,fastq,979886205.0,19213455.0,Heart2 Run2,0:51,A:246169086;C:264387065;G:236377487;T:227289693;N:5662874,51,,,,246169086,264387065,236377487,227289693,5662874,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37935,SRR1554484,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_1.fq.gz,fastq,654412671.0,12831621.0,Brain2 Run1,0:51,A:160544180;C:166355290;G:168608762;T:158684308;N:220131,51,,,,160544180,166355290,168608762,158684308,220131,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,0.0,,0.99993,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37936,SRR1554485,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_2.fq.gz,fastq,856322793.0,16790643.0,Brain2 Run2,0:51,A:210706815;C:226772546;G:212404752;T:201722093;N:4716587,51,,,,210706815,226772546,212404752,201722093,4716587,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37937,SRR1554481,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_1.fq.gz,fastq,116086965.0,2276215.0,Ovary1 Run1,0:51,A:29237121;C:30235277;G:29264328;T:27320814;N:29425,51,,,,29237121,30235277,29264328,27320814,29425,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,9e-05,,0.99967,,0.65,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37938,SRR1554482,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_2.fq.gz,fastq,138905844.0,2723644.0,Ovary1 Run2,0:51,A:34695180;C:38015933;G:33434207;T:32057083;N:703441,51,,,,34695180,38015933,33434207,32057083,703441,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00016,,5e-05,,0.99977,,0.42857,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37939,SRR1554478,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_1.fq.gz,fastq,655515750.0,12853250.0,Testis1 Run1,0:51,A:152422885;C:163771947;G:179144090;T:159997538;N:179290,51,,,,152422885,163771947,179144090,159997538,179290,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0011,,0.00053,,0.99829,,0.67777,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37940,SRR1554479,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_2.fq.gz,fastq,777594399.0,15246949.0,Testis1 Run2,0:51,A:180116528;C:202508153;G:204833105;T:186435696;N:3700917,51,,,,180116528,202508153,204833105,186435696,3700917,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00073,,0.00032,,0.99898,,0.62745,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37941,SRR1554475,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_1.fq.gz,fastq,810162642.0,15885542.0,Heart1 Run1,0:51,A:199665102;C:213941735;G:204361738;T:191870055;N:324012,51,,,,199665102,213941735,204361738,191870055,324012,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,6e-05,,1e-05,,0.99989,,0.8,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37942,SRR1554476,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_2.fq.gz,fastq,1013563698.0,19873798.0,Heart1 Run2,0:51,A:249913434;C:275453651;G:247166233;T:235034199;N:5996181,51,,,,249913434,275453651,247166233,235034199,5996181,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,4e-05,,2e-05,,0.99997,,0.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37943,SRR1554472,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_1.fq.gz,fastq,679860294.0,13330594.0,Brain1 Run1,0:51,A:167202435;C:176450132;G:174468721;T:161497185;N:241821,51,,,,167202435,176450132,174468721,161497185,241821,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37944,SRR1554473,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_2.fq.gz,fastq,838372782.0,16438682.0,Brain1 Run2,0:51,A:206906228;C:221202670;G:210716690;T:195319694;N:4227500,51,,,,206906228,221202670,210716690,195319694,4227500,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
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
39687,SRR2051113,SRX1048368,SRS952733,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P39,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 4,P39,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4090297192.0,40497992.0,P39,0:101,A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421,101,,,,1016157993,993771683,965986507,1113686588,694421,SRX1048368,SRS952733,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9417,,0.14428,,0.68937,,0.5438,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39688,SRR2051110,SRX1048367,SRS952731,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P37,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 3,P37,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4647442886.0,46014286.0,P37,0:101,A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479,101,,,,1149955739,1129088798,1093234722,1274375148,788479,SRX1048367,SRS952731,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94585,,0.12571,,0.68633,,0.52597,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39689,SRR2051112,SRX1048366,SRS952732,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P36,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 2,P36,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4296894611.0,42543511.0,P36,0:101,A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407,101,,,,1050039699,1061123166,1022913715,1162094624,723407,SRX1048366,SRS952732,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94977,,0.13188,,0.70976,,0.52728,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39690,SRR2051109,SRX1048365,SRS952730,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P35,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 1,P35,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4094752706.0,40542106.0,P35,0:101,A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167,101,,,,1009779802,1004374749,969241794,1110655194,701167,SRX1048365,SRS952730,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94442,,0.13203,,0.70023,,0.53953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39691,SRR2051102,SRX1048364,SRS952729,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P29,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 4,P29,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4983571896.0,49342296.0,P29,0:101,A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841,101,,,,1247122516,1202173111,1173654831,1359775597,845841,SRX1048364,SRS952729,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94329,,0.13234,,0.68286,,0.51586,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39692,SRR2051100,SRX1048363,SRS952727,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P28,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 3,P28,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4032678914.0,39927514.0,P28,0:101,A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488,101,,,,1015356577,970369004,937306142,1108957703,689488,SRX1048363,SRS952727,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93887,,0.13869,,0.69079,,0.52237,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39693,SRR2051101,SRX1048362,SRS952728,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P26,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 2,P26,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz,fastq fastq fastq fastq,6526758875.0,64621375.0,P26,0:101,A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228,101,,,,1635664768,1568967965,1518148006,1802863908,1114228,SRX1048362,SRS952728,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93822,,0.15203,,0.68609,,0.53171,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39694,SRR2051096,SRX1048361,SRS952726,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P25,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 1,P25,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4185957322.0,41445122.0,P25,0:101,A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428,101,,,,1081936223,978799105,956795307,1167714259,712428,SRX1048361,SRS952726,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9288,,0.17032,,0.6801,,0.51298,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39695,SRR2051095,SRX1048360,SRS952725,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P19,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 4,P19,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4293546461.0,42510361.0,P19,0:101,A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822,101,,,,1062707728,1045602693,1011860446,1172670772,704822,SRX1048360,SRS952725,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94381,,0.13697,,0.69051,,0.51415,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39696,SRR2051094,SRX1048359,SRS952724,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P18,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 3,P18,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4257944163.0,42157863.0,P18,0:101,A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125,101,,,,1044532409,1049992329,1010166097,1152524203,729125,SRX1048359,SRS952724,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94262,,0.14592,,0.69014,,0.52498,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39697,SRR2051093,SRX1048358,SRS952723,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P17,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 2,P17,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4278385553.0,42360253.0,P17,0:101,A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139,101,,,,1040955882,1060023973,1019487833,1157186726,731139,SRX1048358,SRS952723,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94697,,0.14458,,0.69643,,0.53451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39698,SRR2051092,SRX1048357,SRS952722,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P15,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 1,P15,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4341747499.0,42987599.0,P15,0:101,A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377,101,,,,1052621077,1088380866,1041958433,1158051746,735377,SRX1048357,SRS952722,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94563,,0.153,,0.69822,,0.54133,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39699,SRR2051091,SRX1048356,SRS952721,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN9,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 4,CN9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4220387212.0,41786012.0,CN9,0:101,A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235,101,,,,1031722430,1044497851,1005706674,1137783022,677235,SRX1048356,SRS952721,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.95231,,0.14084,,0.69682,,0.52966,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39700,SRR2051090,SRX1048354,SRS952719,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN8,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 3,CN8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,5835502553.0,57777253.0,CN8,0:101,A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739,101,,,,1424369529,1441755207,1391851806,1576540272,985739,SRX1048354,SRS952719,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94643,,0.12925,,0.70725,,0.52949,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39701,SRR2050894,SRX1048353,SRS952718,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN7,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 2,CN7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4789094477.0,47416777.0,CN7,0:101,A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016,101,,,,1160528098,1197558725,1155573375,1274638263,796016,SRX1048353,SRS952718,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9501,,0.14828,,0.69966,,0.52764,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39702,SRR2050892,SRX1048352,SRS952717,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN5,,breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 1,CN5,CN5 EL4506 TGACCA,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4526144512.0,44813312.0,CN5,0:101,A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159,101,,,,1109966549,1116619353,1075422479,1223366972,769159,SRX1048352,SRS952717,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94604,,0.14084,,0.69004,,0.53407,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures