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
9367,ERR145653,ERX121572,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 B seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_B_1.fq.gz WW3_B_2.fq.gz,fastq fastq,4347695086.0,21523243.0,E MTAB 1155:WW3 B,0:101 1:101,A:1074237454;C:1092333862;G:1102729864;T:1065390007;N:13003899,101,101,,,1074237454,1092333862,1102729864,1065390007,13003899,ERX121572,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95796,0.9583,0.02413,0.02313,0.83946,0.8338,0.51717,0.51633,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9368,ERR145654,ERX121560,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 A seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_A_1.fq.gz WW4_A_2.fq.gz,fastq fastq,80948470.0,400735.0,E MTAB 1155:WW4 A,0:101 1:101,A:21174054;C:19268727;G:19622428;T:20880804;N:2457,101,101,,,21174054,19268727,19622428,20880804,2457,ERX121560,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93674,0.92652,0.0383,0.03971,0.84776,0.86028,0.52028,0.51601,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9369,ERR145639,ERX121583,ERS151247,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW4 F M pooled fish,SAMEA1487357,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487357|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW4 seq,CW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW4_1.fq.gz CW4_2.fq.gz,fastq fastq,7322391324.0,36249462.0,E MTAB 1155:CW4,0:101 1:101,A:1915177797;C:1750141576;G:1768328049;T:1887892000;N:851902,101,101,,,1915177797,1750141576,1768328049,1887892000,851902,ERX121583,ERS151247,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94177,0.93855,0.04669,0.04835,0.81227,0.81663,0.5297,0.53381,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9370,ERR145632,ERX121582,ERS151246,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH2 F M pooled fish,SAMEA1487358,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487358|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH2 seq,CH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH2_1.fq.gz CH2_2.fq.gz,fastq fastq,6008384960.0,29744480.0,E MTAB 1155:CH2,0:101 1:101,A:1551084475;C:1456651824;G:1467972620;T:1531930144;N:745897,101,101,,,1551084475,1456651824,1467972620,1531930144,745897,ERX121582,ERS151246,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94484,0.94325,0.04187,0.04238,0.81448,0.8172,0.46639,0.50253,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9371,ERR145634,ERX121581,ERS151245,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH4 F M pooled fish,SAMEA1487361,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487361|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH4 seq,CH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH4_1.fq.gz CH4_2.fq.gz,fastq fastq,5647385104.0,27957352.0,E MTAB 1155:CH4,0:101 1:101,A:1469982057;C:1356659164;G:1371916498;T:1448143269;N:684116,101,101,,,1469982057,1356659164,1371916498,1448143269,684116,ERX121581,ERS151245,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93865,0.93633,0.0439,0.04446,0.80549,0.80864,0.53045,0.51098,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9372,ERR145651,ERX121579,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 B seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_B_1.fq.gz WW2_B_2.fq.gz,fastq fastq,4738967672.0,23460236.0,E MTAB 1155:WW2 B,0:101 1:101,A:1175576318;C:1183749238;G:1198839519;T:1166587116;N:14215481,101,101,,,1175576318,1183749238,1198839519,1166587116,14215481,ERX121579,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95497,0.95617,0.02438,0.0233,0.82909,0.82455,0.51164,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9373,ERR145652,ERX121578,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 A seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_A_1.fq.gz WW3_A_2.fq.gz,fastq fastq,229808532.0,1137666.0,E MTAB 1155:WW3 A,0:101 1:101,A:59360822;C:55502890;G:56337453;T:58600433;N:6934,101,101,,,59360822,55502890,56337453,58600433,6934,ERX121578,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93623,0.92715,0.03151,0.03268,0.83735,0.84952,0.52265,0.5038,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9374,ERR145649,ERX121577,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 B seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_B_1.fq.gz WW1_B_2.fq.gz,fastq fastq,7635373356.0,37798878.0,E MTAB 1155:WW1 B,0:101 1:101,A:1902965653;C:1900547622;G:1920575326;T:1888470954;N:22813801,101,101,,,1902965653,1900547622,1920575326,1888470954,22813801,ERX121577,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95977,0.95988,0.02636,0.02563,0.84279,0.83808,0.52131,0.45646,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9375,ERR145636,ERX121576,ERS151244,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW2 F M pooled fish,SAMEA1487364,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487364|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW2 seq,CW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW2_1.fq.gz CW2_2.fq.gz,fastq fastq,7748012798.0,38356499.0,E MTAB 1155:CW2,0:101 1:101,A:2015650126;C:1864022271;G:1874527501;T:1992894699;N:918201,101,101,,,2015650126,1864022271,1874527501,1992894699,918201,ERX121576,ERS151244,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94537,0.94243,0.04249,0.04301,0.82213,0.82552,0.52811,0.53747,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9376,ERR145646,ERX121571,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 A seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_A_1.fq.gz WH4_A_2.fq.gz,fastq fastq,812883148.0,4024174.0,E MTAB 1155:WH4 A,0:101 1:101,A:209997189;C:196285019;G:198925947;T:207278009;N:396984,101,101,,,209997189,196285019,198925947,207278009,396984,ERX121571,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94663,0.91942,0.03602,0.03591,0.8424,0.85462,0.51702,0.51147,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9377,ERR145647,ERX121570,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 B seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_B_1.fq.gz WH4_B_2.fq.gz,fastq fastq,10768144694.0,53307647.0,E MTAB 1155:WH4 B,0:101 1:101,A:2682817583;C:2706807352;G:2714533015;T:2652309644;N:11677100,101,101,,,2682817583,2706807352,2714533015,2652309644,11677100,ERX121570,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95867,0.96056,0.02378,0.02413,0.83609,0.83889,0.43331,0.44066,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9378,ERR145655,ERX121569,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 B seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_B_1.fq.gz WW4_B_2.fq.gz,fastq fastq,6455936968.0,31960084.0,E MTAB 1155:WW4 B,0:101 1:101,A:1610738878;C:1605252294;G:1623372987;T:1597311219;N:19261590,101,101,,,1610738878,1605252294,1623372987,1597311219,19261590,ERX121569,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.96085,0.96101,0.02863,0.02731,0.84995,0.8452,0.52157,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9379,ERR145633,ERX121568,ERS151240,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH3 F M pooled fish,SAMEA1487363,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487363|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH3 seq,CH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH3_1.fq.gz CH3_2.fq.gz,fastq fastq,6146419640.0,30427820.0,E MTAB 1155:CH3,0:101 1:101,A:1596666196;C:1479913350;G:1493612614;T:1575480940;N:746540,101,101,,,1596666196,1479913350,1493612614,1575480940,746540,ERX121568,ERS151240,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93901,0.93723,0.04362,0.04417,0.79715,0.7977,0.51473,0.52412,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9380,ERR145650,ERX121567,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 A seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_A_1.fq.gz WW2_A_2.fq.gz,fastq fastq,280038054.0,1386327.0,E MTAB 1155:WW2 A,0:101 1:101,A:72831492;C:67021049;G:68232991;T:71942949;N:9573,101,101,,,72831492,67021049,68232991,71942949,9573,ERX121567,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93032,0.9187,0.03207,0.03356,0.82852,0.84139,0.52376,0.52436,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9381,ERR145637,ERX121565,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 A seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_A_1.fq.gz CW3_A_2.fq.gz,fastq fastq,2104292580.0,10417290.0,E MTAB 1155:CW3 A,0:101 1:101,A:547829220;C:504948167;G:510803037;T:540521191;N:190965,101,101,,,547829220,504948167,510803037,540521191,190965,ERX121565,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93423,0.92981,0.04776,0.04835,0.81245,0.81471,0.51349,0.4822,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9382,ERR145631,ERX121564,ERS151237,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH1 F M pooled fish,SAMEA1487356,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487356|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH1 seq,CH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH1_1.fq.gz CH1_2.fq.gz,fastq fastq,7734471526.0,38289463.0,E MTAB 1155:CH1,0:101 1:101,A:1980474194;C:1892305985;G:1907192207;T:1953595996;N:903144,101,101,,,1980474194,1892305985,1907192207,1953595996,903144,ERX121564,ERS151237,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94403,0.94213,0.03862,0.03913,0.82309,0.82556,0.49626,0.49773,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9383,ERR145635,ERX121562,ERS151235,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW1 F M pooled fish,SAMEA1487366,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487366|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW1 seq,CW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW1_1.fq.gz CW1_2.fq.gz,fastq fastq,6202716838.0,30706519.0,E MTAB 1155:CW1,0:101 1:101,A:1612950873;C:1492406749;G:1504306823;T:1592361004;N:691389,101,101,,,1612950873,1492406749,1504306823,1592361004,691389,ERX121562,ERS151235,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94448,0.94226,0.04304,0.04379,0.81296,0.81489,0.5237,0.52588,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9384,ERR145648,ERX121561,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 A seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_A_1.fq.gz WW1_A_2.fq.gz,fastq fastq,330954174.0,1638387.0,E MTAB 1155:WW1 A,0:101 1:101,A:86485807;C:78916128;G:80103844;T:85437370;N:11025,101,101,,,86485807,78916128,80103844,85437370,11025,ERX121561,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93321,0.92294,0.03445,0.03581,0.84133,0.85267,0.54253,0.53593,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9385,ERR145638,ERX121559,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 B seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_B_1.fq.gz CW3_B_2.fq.gz,fastq fastq,6504819756.0,32202078.0,E MTAB 1155:CW3 B,0:101 1:101,A:1653674963;C:1600212014;G:1606437826;T:1637400265;N:7094688,101,101,,,1653674963,1600212014,1606437826,1637400265,7094688,ERX121559,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94253,0.94443,0.03782,0.03856,0.80661,0.80801,0.49414,0.51667,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9386,ERR147028,ERX122956,ERS151238,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH3 F M pooled fish,SAMEA1487362,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH3 seq,WH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH3_1.fq.gz WH3_2.fq.gz,fastq fastq,3197103894.0,15827247.0,E MTAB 1155:WH3,0:101 1:101,A:829020337;C:767623553;G:780642278;T:818288216;N:1529510,101,101,,,829020337,767623553,780642278,818288216,1529510,ERX122956,ERS151238,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94791,0.91975,0.03726,0.03735,0.84291,0.85622,0.4972,0.50314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9387,ERR147027,ERX122955,ERS151236,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH2 F M pooled fish,SAMEA1487365,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487365|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH2 seq,WH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH2_1.fq.gz WH2_2.fq.gz,fastq fastq,3455989922.0,17108861.0,E MTAB 1155:WH2,0:101 1:101,A:902145358;C:824320050;G:837200815;T:890816825;N:1506874,101,101,,,902145358,824320050,837200815,890816825,1506874,ERX122955,ERS151236,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94863,0.92001,0.04084,0.04066,0.83796,0.85263,0.5275,0.51735,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9388,ERR147026,ERX122954,ERS151243,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH1 F M pooled fish,SAMEA1487369,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487369|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH1 seq,WH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH1_1.fq.gz WH1_2.fq.gz,fastq fastq,3005524064.0,14878832.0,E MTAB 1155:WH1,0:101 1:101,A:780146739;C:722416478;G:730307409;T:771476282;N:1177156,101,101,,,780146739,722416478,730307409,771476282,1177156,ERX122954,ERS151243,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94764,0.92072,0.03746,0.03773,0.83416,0.84831,0.42239,0.51505,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9711,ERR3366000,ERX3390288,ERS3506636,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 3,SAMEA5702979,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 3 p,WT 5dpf whole 3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz,fastq fastq,7638506536.0,25293068.0,E MTAB 8029:WT 5dpf whole 3 ,0:151 1:151,A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553,151,151,,,2033085216,1787203019,1834311569,1982924179,982553,ERX3390288,ERS3506636,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92943,0.93349,0.06443,0.06476,0.67008,0.68489,0.45244,0.47512,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9712,ERR3365999,ERX3390287,ERS3506635,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 2,SAMEA5702978,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 2 p,WT 5dpf whole 2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz,fastq fastq,8029356446.0,26587273.0,E MTAB 8029:WT 5dpf whole 2 ,0:151 1:151,A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810,151,151,,,2111720421,1902949602,1956400199,2057162414,1123810,ERX3390287,ERS3506635,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93664,0.9394,0.06211,0.06234,0.67036,0.68416,0.44709,0.4713,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9713,ERR3365998,ERX3390286,ERS3506634,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 1,SAMEA5702977,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 1 p,WT 5dpf whole 1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz,fastq fastq,7581314682.0,25103691.0,E MTAB 8029:WT 5dpf whole 1 ,0:151 1:151,A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540,151,151,,,2028089715,1768357820,1809746152,1974047455,1073540,ERX3390286,ERS3506634,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92712,0.93122,0.06876,0.06853,0.66464,0.67537,0.46592,0.47176,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9714,ERR3365997,ERX3390285,ERS3506633,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl2,SAMEA5702976,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl2 p,c386C T het 5dpf whl2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz,fastq fastq,7431512716.0,24607658.0,E MTAB 8029:c386C T het 5dpf whl 2 ,0:151 1:151,A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572,151,151,,,1981584337,1740735155,1776201259,1931922393,1069572,ERX3390285,ERS3506633,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92957,0.933,0.0653,0.06445,0.66967,0.6788,0.46228,0.46392,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9715,ERR3365996,ERX3390284,ERS3506632,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl1,SAMEA5702975,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl1 p,c386C T het 5dpf whl1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz,fastq fastq,7350140024.0,24338212.0,E MTAB 8029:c386C T het 5dpf whl 1 ,0:151 1:151,A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274,151,151,,,1930881649,1748604586,1790297791,1879354724,1001274,ERX3390284,ERS3506632,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93663,0.9384,0.05835,0.05828,0.66557,0.67588,0.467,0.46407,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9716,ERR3365995,ERX3390283,ERS3506631,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c.386C T het 5dpf whl3,SAMEA5702974,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c.386C T het 5dpf whl3 p,c.386C T het 5dpf whl3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz,fastq fastq,6059681642.0,20065171.0,E MTAB 8029:c386C T het 5dpf whl 3 ,0:151 1:151,A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092,151,151,,,1604034432,1423963595,1467519505,1563303018,861092,ERX3390283,ERS3506631,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93301,0.9374,0.0658,0.06581,0.66681,0.68503,0.46139,0.47743,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10374,ERR8058375,ERX7625096,ERS10119356,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 3,SAMEA12512752,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 3 p,Morphine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz,fastq fastq,11175776640.0,44348320.0,E MTAB 11346:NG 10331 4M lib138515 4790 6 ,0:126 1:126,A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329,126,126,,,3058552548,2537121022,2531362154,3047376587,1364329,ERX7625096,ERS10119356,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93345,0.93836,0.09826,0.09482,0.69497,0.69968,0.46885,0.46966,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10375,ERR8058374,ERX7625095,ERS10119355,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 2,SAMEA12512751,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 2 p,Morphine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz,fastq fastq,10428424776.0,41382638.0,E MTAB 11346:NG 10331 3M lib138512 4790 5 ,0:126 1:126,A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201,126,126,,,2840226558,2379827926,2389813154,2817428937,1128201,ERX7625095,ERS10119355,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94204,0.9476,0.09827,0.09565,0.7008,0.70483,0.47435,0.47651,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10376,ERR8058373,ERX7625094,ERS10119354,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 1,SAMEA12512750,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 1 p,Morphine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz,fastq fastq,13158093312.0,52214656.0,E MTAB 11346:NG 10331 2M lib138509 4790 5 ,0:126 1:126,A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572,126,126,,,3613282182,2969954628,2964948806,3608471124,1436572,ERX7625094,ERS10119354,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93755,0.93735,0.11204,0.10849,0.67838,0.68335,0.45142,0.46509,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10377,ERR8058372,ERX7625093,ERS10119353,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 3,SAMEA12512749,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 3 p,Control 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz,fastq fastq,14106514968.0,55978234.0,E MTAB 11346:NG 10331 4C lib138514 4790 6 ,0:126 1:126,A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393,126,126,,,3862641975,3195634147,3187866318,3858673135,1699393,ERX7625093,ERS10119353,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93657,0.93813,0.09783,0.09438,0.68925,0.69605,0.4741,0.47037,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10378,ERR8058371,ERX7625092,ERS10119352,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 2,SAMEA12512748,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 2 p,Control 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz,fastq fastq,8889952680.0,35277590.0,E MTAB 11346:NG 10331 3C lib138511 4790 5 ,0:126 1:126,A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902,126,126,,,2424658667,2024699093,2023098669,2416527349,968902,ERX7625092,ERS10119352,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94168,0.94149,0.09632,0.09404,0.68996,0.69672,0.46007,0.47123,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10379,ERR8058370,ERX7625091,ERS10119351,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 1,SAMEA12512747,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 1 p,Control 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz,fastq fastq,12714421356.0,50454053.0,E MTAB 11346:NG 10331 2C lib138508 4790 5 ,0:126 1:126,A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272,126,126,,,3470625985,2894721473,2886656166,3461036460,1381272,ERX7625091,ERS10119351,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93951,0.93975,0.10489,0.10173,0.68134,0.68702,0.45337,0.44545,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10380,ERR8058369,ERX7625090,ERS10119350,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 3,SAMEA12512746,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 3 p,Cocaine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz,fastq fastq,9574359984.0,37993492.0,E MTAB 11346:NG 10331 4CC lib138516 4790 6 ,0:126 1:126,A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518,126,126,,,2623103101,2170327733,2166494677,2613276955,1157518,ERX7625090,ERS10119350,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.9366,0.93856,0.10196,0.09901,0.69018,0.69611,0.46501,0.46917,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10381,ERR8058368,ERX7625089,ERS10119349,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 2,SAMEA12512745,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 2 p,Cocaine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz,fastq fastq,6977861604.0,27689927.0,E MTAB 11346:NG 10331 3CC lib138513 4828 1 ,0:126 1:126,A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359,126,126,,,1938593544,1560242508,1564690065,1913028128,1307359,ERX7625089,ERS10119349,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94226,0.9472,0.10354,0.10202,0.69911,0.69891,0.4749,0.47595,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10382,ERR8058367,ERX7625088,ERS10119348,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 1,SAMEA12512744,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 1 p,Cocaine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz,fastq fastq,13608728532.0,54002891.0,E MTAB 11346:NG 10331 2CC lib138510 4790 5 ,0:126 1:126,A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601,126,126,,,3713185950,3097562409,3088976816,3707538756,1464601,ERX7625088,ERS10119348,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93921,0.94011,0.104,0.10075,0.68043,0.68523,0.44482,0.4591,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
11747,ERR11608177,ERX11010308,ERS15939662,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU2,SAMEA113945412,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945412|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU2|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU2|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU2 p,MU2 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU2_R1.fastq.gz MU2_R2.fastq.gz,fastq fastq,8373912900.0,27913043.0,E MTAB 13116:MU2 R,0:150 1:150,A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489,150,150,,,2149105370,2028251580,2055193482,2141168979,193489,ERX11010308,ERS15939662,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11748,ERR11608179,ERX11010310,ERS15939664,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT1,SAMEA113945414,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945414|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:WT1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:WT1|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT1 p,WT1 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT1_R1.fastq.gz WT1_R2.fastq.gz,fastq fastq,6729388500.0,22431295.0,E MTAB 13116:WT1 R,0:150 1:150,A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873,150,150,,,1730015872,1621295817,1657133586,1720858352,84873,ERX11010310,ERS15939664,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11749,ERR11608176,ERX11010307,ERS15939661,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU1,SAMEA113945411,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945411|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU1|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU1 p,MU1 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU1_R1.fastq.gz MU1_R2.fastq.gz,fastq fastq,7310352000.0,24367840.0,E MTAB 13116:MU1 R,0:150 1:150,A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432,150,150,,,1888660247,1748082353,1788562372,1884958596,88432,ERX11010307,ERS15939661,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11750,ERR11608178,ERX11010309,ERS15939663,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU3,SAMEA113945413,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945413|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU3|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU3|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU3 p,MU3 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU3_R1.fastq.gz MU3_R2.fastq.gz,fastq fastq,8826207900.0,29420693.0,E MTAB 13116:MU3 R,0:150 1:150,A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162,150,150,,,2298326835,2100185951,2130807919,2296678033,209162,ERX11010309,ERS15939663,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11751,ERR11608180,ERX11010311,ERS15939665,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT2,E MTAB 13116:WT2,,strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT2 p,WT2 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT2_R1.fastq.gz WT2_R2.fastq.gz,fastq fastq,8368621500.0,27895405.0,E MTAB 13116:WT2 R,0:150 1:150,A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219,150,150,,,2126734187,2050458346,2078646608,2112586140,196219,ERX11010311,ERS15939665,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11752,ERR11608181,ERX11010312,ERS15939666,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT3,E MTAB 13116:WT3,,strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT3 p,WT3 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT3_R1.fastq.gz WT3_R2.fastq.gz,fastq fastq,8718445500.0,29061485.0,E MTAB 13116:WT3 R,0:150 1:150,A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540,150,150,,,2244668655,2103611849,2135345835,2234609621,209540,ERX11010312,ERS15939666,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
32018,SRR28960817,SRX24490444,SRS21239720,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 2,,strain:wild type|isolate:10|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 2,Empty RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V2_2.fastq.gz C-V2_1.fastq.gz,fastq fastq,4988932790.0,16519645.0,C V2 1.fastq.gz,0:151 1:151,A:1355149914;C:1135513565;G:1149109922;T:1349135360;N:24029,151,151,,,1355149914,1135513565,1149109922,1349135360,24029,SRX24490444,SRS21239720,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94379,0.94549,0.11621,0.11505,0.65423,0.65577,0.48135,0.48232,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32019,SRR28960818,SRX24490443,SRS21239719,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 1,,strain:wild type|isolate:9|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 1,Empty RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V1_2.fastq.gz C-V1_1.fastq.gz,fastq fastq,5032900970.0,16665235.0,C V1 1.fastq.gz,0:151 1:151,A:1378766254;C:1133849186;G:1146563693;T:1373698300;N:23537,151,151,,,1378766254,1133849186,1146563693,1373698300,23537,SRX24490443,SRS21239719,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9444,0.94533,0.11258,0.11038,0.65194,0.65259,0.48812,0.48428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32020,SRR28960819,SRX24490442,SRS21239718,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C4,,strain:wild type|isolate:8|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C4,igldcp C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C4_2.fastq.gz G17-C4_1.fastq.gz,fastq fastq,5008644028.0,16584914.0,G17 C4 1.fastq.gz,0:151 1:151,A:1365541116;C:1135139643;G:1150040618;T:1357899842;N:22809,151,151,,,1365541116,1135139643,1150040618,1357899842,22809,SRX24490442,SRS21239718,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94527,0.94533,0.10689,0.10479,0.65535,0.65681,0.47637,0.48487,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32021,SRR28960820,SRX24490441,SRS21239717,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C3,,strain:wild type|isolate:7|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C3,igldcp C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C3_2.fastq.gz G17-C3_1.fastq.gz,fastq fastq,4980119222.0,16490461.0,G17 C3 1.fastq.gz,0:151 1:151,A:1360303556;C:1126738486;G:1145297479;T:1347756591;N:23110,151,151,,,1360303556,1126738486,1145297479,1347756591,23110,SRX24490441,SRS21239717,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9466,0.94717,0.11289,0.11094,0.66257,0.66464,0.47181,0.47916,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32022,SRR28960821,SRX24490440,SRS21239716,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C2,,strain:wild type|isolate:6|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C2,igldcp C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C2_2.fastq.gz G17-C2_1.fastq.gz,fastq fastq,5007933422.0,16582561.0,G17 C2 1.fastq.gz,0:151 1:151,A:1372213671;C:1129918132;G:1143655284;T:1362122899;N:23436,151,151,,,1372213671,1129918132,1143655284,1362122899,23436,SRX24490440,SRS21239716,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94572,0.94517,0.11003,0.10818,0.65658,0.65805,0.4773,0.48344,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32023,SRR28960822,SRX24490439,SRS21239715,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C1,,strain:wild type|isolate:5|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C1,igldcp C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C1_1.fastq.gz G17-C1_2.fastq.gz,fastq fastq,5024913070.0,16638785.0,G17 C1 1.fastq.gz,0:151 1:151,A:1380366672;C:1129585807;G:1150817244;T:1364119307;N:24040,151,151,,,1380366672,1129585807,1150817244,1364119307,24040,SRX24490439,SRS21239715,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94287,0.94431,0.11558,0.11383,0.65277,0.65382,0.4826,0.48102,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32024,SRR28960823,SRX24490438,SRS21239714,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C4,,strain:wild type|isolate:4|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C4,Empty C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C4_2.fastq.gz C-C4_1.fastq.gz,fastq fastq,4979945874.0,16489887.0,C C4 1.fastq.gz,0:151 1:151,A:1355600042;C:1132041799;G:1147315384;T:1344965018;N:23631,151,151,,,1355600042,1132041799,1147315384,1344965018,23631,SRX24490438,SRS21239714,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94757,0.94857,0.10346,0.10203,0.65539,0.65673,0.4708,0.46117,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32025,SRR28960827,SRX24490437,SRS21239713,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C3,,strain:wild type|isolate:3|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C3,Empty C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C3_2.fastq.gz C-C3_1.fastq.gz,fastq fastq,5029174894.0,16652897.0,C C3 1.fastq.gz,0:151 1:151,A:1374911488;C:1136783068;G:1150269816;T:1367186209;N:24313,151,151,,,1374911488,1136783068,1150269816,1367186209,24313,SRX24490437,SRS21239713,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94336,0.94484,0.11529,0.11371,0.65305,0.65488,0.47386,0.4875,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32026,SRR28960824,SRX24490436,SRS21239712,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 4,,strain:wild type|isolate:15|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 4,igldcp RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V4_1.fastq.gz G17-V4_2.fastq.gz,fastq fastq,5038044634.0,16682267.0,G17 V4 1.fastq.gz,0:151 1:151,A:1373754614;C:1142848550;G:1159235100;T:1362182221;N:24149,151,151,,,1373754614,1142848550,1159235100,1362182221,24149,SRX24490436,SRS21239712,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94236,0.94358,0.10841,0.10623,0.65429,0.65512,0.47952,0.47896,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32027,SRR28960825,SRX24490435,SRS21239711,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 2,,strain:wild type|isolate:14|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 2,igldcp RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V2_2.fastq.gz G17-V2_1.fastq.gz,fastq fastq,4992836442.0,16532571.0,G17 V2 1.fastq.gz,0:151 1:151,A:1370989397;C:1121917932;G:1135482493;T:1364423268;N:23352,151,151,,,1370989397,1121917932,1135482493,1364423268,23352,SRX24490435,SRS21239711,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94244,0.94361,0.11703,0.11517,0.65297,0.65305,0.47906,0.47762,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32028,SRR28960826,SRX24490434,SRS21239710,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 1,,strain:wild type|isolate:13|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 1,igldcp RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V1_2.fastq.gz G17-V1_1.fastq.gz,fastq fastq,5022577402.0,16631051.0,G17 V1 1.fastq.gz,0:151 1:151,A:1373133624;C:1136711402;G:1147351250;T:1365356916;N:24210,151,151,,,1373133624,1136711402,1147351250,1365356916,24210,SRX24490434,SRS21239710,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94548,0.9457,0.11091,0.10876,0.6566,0.65794,0.47672,0.47334,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32029,SRR28960828,SRX24490433,SRS21239709,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 4,,strain:wild type|isolate:12|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 4,Empty RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V4_1.fastq.gz C-V4_2.fastq.gz,fastq fastq,4996580940.0,16544970.0,C V4 1.fastq.gz,0:151 1:151,A:1365771383;C:1129645420;G:1139771568;T:1361369690;N:22879,151,151,,,1365771383,1129645420,1139771568,1361369690,22879,SRX24490433,SRS21239709,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94201,0.94399,0.10865,0.10729,0.65295,0.65397,0.47378,0.48264,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32030,SRR28960829,SRX24490432,SRS21239708,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 3,,strain:wild type|isolate:11|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 3,Empty RGNNV 3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V3_1.fastq.gz C-V3_2.fastq.gz,fastq fastq,4990782540.0,16525770.0,C V3 1.fastq.gz,0:151 1:151,A:1370883963;C:1121960304;G:1139361266;T:1358553278;N:23729,151,151,,,1370883963,1121960304,1139361266,1358553278,23729,SRX24490432,SRS21239708,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94311,0.94426,0.10644,0.10476,0.65535,0.65756,0.46134,0.44955,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32031,SRR28960830,SRX24490431,SRS21239707,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C2,,strain:wild type|isolate:2|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C2,Empty C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C2_2.fastq.gz C-C2_1.fastq.gz,fastq fastq,4991313154.0,16527527.0,C C2 1.fastq.gz,0:151 1:151,A:1366713096;C:1125818845;G:1141236594;T:1357520576;N:24043,151,151,,,1366713096,1125818845,1141236594,1357520576,24043,SRX24490431,SRS21239707,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94263,0.94476,0.10847,0.10745,0.65928,0.65904,0.47366,0.47959,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32032,SRR28960831,SRX24490430,SRS21239702,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C1,,strain:wild type|isolate:1|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C1,Empty C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C1_1.fastq.gz C-C1_2.fastq.gz,fastq fastq,5031068434.0,16659167.0,C C1 1.fastq.gz,0:151 1:151,A:1369231804;C:1143688515;G:1163238884;T:1354885267;N:23964,151,151,,,1369231804,1143688515,1163238884,1354885267,23964,SRX24490430,SRS21239702,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94547,0.94589,0.10958,0.10835,0.6564,0.6565,0.48608,0.48591,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
39756,SRR2125736,SRX1117105,SRS1010315,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,Polr1c2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish Polr1c2|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Polr1c2,RNA Seq of Polr1c2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,Polr1c2_S2_L001_R1_001.fastq.gz Polr1c2_S2_L001_R2_001.fastq.gz,bam fastq,1024040592.0,3467167.0,RNA Seq of Polr1c2,0:147.69 1:147.67,A:280222262;C:231619577;G:229733851;T:282415559;N:49343,147,147,,,280222262,231619577,229733851,282415559,49343,SRX1117105,SRS1010315,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.94843,0.95151,0.09589,0.09554,0.68747,0.68694,0.48798,0.48429,150,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
39757,SRR2125735,SRX1117104,SRS1010314,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,polr1cKO,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of polr1cKO|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of polr1cKO,RNA Seq of polr1cKO,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,polr1cKO_S2_L001_R2_001.fastq.gz polr1cKO_S2_L001_R1_001.fastq.gz,fastq fastq,2153644339.0,7160972.0,RNA Seq of polr1cKO,0:150.40 1:150.34,A:558724957;C:517375772;G:514543839;T:562990605;N:9166,150,150,,,558724957,517375772,514543839,562990605,9166,SRX1117104,SRS1010314,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95998,0.9611,0.07455,0.0729,0.65354,0.65496,0.45853,0.46158,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39758,SRR2125734,SRX1117103,SRS1010313,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,AB2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of AB2|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB2,RNA Seq of AB2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,AB2_S1_L001_R2_001.fastq.gz AB2_S1_L001_R1_001.fastq.gz,fastq fastq,829696252.0,2784590.0,RNA Seq of AB2,0:149.00 1:148.96,A:218353676;C:195998962;G:195017076;T:220297820;N:28718,149,148,,,218353676,195998962,195017076,220297820,28718,SRX1117103,SRS1010313,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96274,0.96494,0.05571,0.05462,0.73588,0.73657,0.48938,0.48219,149,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39759,SRR2125733,SRX1117102,SRS1010312,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,WT,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of WT|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of WT,RNA Seq of WT,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,wt_S1_L001_R1_001.fastq.gz wt_S1_L001_R2_001.fastq.gz,fastq fastq,1937209279.0,6445507.0,RNA Seq of WT,0:150.30 1:150.25,A:496555264;C:470694471;G:467911055;T:502040892;N:7597,150,150,,,496555264,470694471,467911055,502040892,7597,SRX1117102,SRS1010312,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95931,0.96087,0.06913,0.06787,0.66101,0.66431,0.45529,0.4629,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
42097,SRR5483549,SRX2766898,SRS2151000,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C1 CGATGT L001 R1 001,C1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC1L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C1 CGATGT L001,C1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C1_CGATGT_L001_R1_001.fastq C1_CGATGT_L001_R2_001.fastq C1_CGATGT_L002_R1_001.fastq C1_CGATGT_L002_R2_001.fastq,fastq fastq fastq fastq,1411679200.0,14356543.0,C1 CGATGT L001 R2 001.fastq,,A:371472311;C:327400140;G:335224751;T:377147836;N:434162,,,,,371472311,327400140,335224751,377147836,434162,SRX2766898,SRS2151000,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93533,0.94243,0.07183,0.07215,0.72111,0.72251,0.46894,0.47065,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
42098,SRR5483548,SRX2766897,SRS2150999,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C2 CGATGT L001 R1 001,C2,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC2L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C2 CGATGT L001,C2 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C2_TGACCA_L001_R1_001.fastq C2_TGACCA_L001_R2_001.fastq C2_TGACCA_L002_R1_001.fastq C2_TGACCA_L002_R2_001.fastq,fastq fastq fastq fastq,1242565800.0,12898403.0,C2 TGACCA L001 R1 001.fastq,,A:326022462;C:289113775;G:293830205;T:333244455;N:354903,,,,,326022462,289113775,293830205,333244455,354903,SRX2766897,SRS2150999,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93498,0.94161,0.07112,0.0695,0.72693,0.72717,0.46957,0.48109,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42099,SRR5483547,SRX2766896,SRS2150998,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C4 CGATGT L001 R1 001,C4,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC4L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C4 CGATGT L001,C4 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C4_GCCAAT_L001_R1_001.fastq C4_GCCAAT_L001_R2_001.fastq C4_GCCAAT_L002_R1_001.fastq C4_GCCAAT_L002_R2_001.fastq,fastq fastq fastq fastq,1185823950.0,12152845.0,C4 GCCAAT L001 R2 001.fastq,,A:314615152;C:271806853;G:280914266;T:318186592;N:301087,,,,,314615152,271806853,280914266,318186592,301087,SRX2766896,SRS2150998,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93274,0.94146,0.07722,0.07634,0.7223,0.72358,0.48559,0.48318,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42100,SRR5483546,SRX2766895,SRS2150996,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C5 CGATGT L001 R1 001,C5,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC5L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C5 CGATGT L001,C5 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C5_ACTTGA_L001_R1_001.fastq C5_ACTTGA_L001_R2_001.fastq C5_ACTTGA_L002_R1_001.fastq C5_ACTTGA_L002_R2_001.fastq,fastq fastq fastq fastq,1107911114.0,11470347.0,C5 ACTTGA L001 R1 001.fastq,,A:291142814;C:256111405;G:262122909;T:298258834;N:275152,,,,,291142814,256111405,262122909,298258834,275152,SRX2766895,SRS2150996,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93423,0.94182,0.07555,0.07453,0.72344,0.72579,0.47773,0.47732,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42101,SRR5483545,SRX2766894,SRS2150997,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C6 CGATGT L001 R1 001,C6,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC6L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C6 CGATGT L001,C6 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C6_TAGCTT_L001_R1_001.fastq C6_TAGCTT_L002_R1_001.fastq C6_TAGCTT_L002_R2_001.fastq C6_TAGCTT_L001_R2_001.fastq,fastq fastq fastq fastq,1083109717.0,10884377.0,C6 TAGCTT L001 R2 001.fastq,,A:285687095;C:248867355;G:257309681;T:290972966;N:272620,,,,,285687095,248867355,257309681,290972966,272620,SRX2766894,SRS2150997,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.9312,0.94054,0.07791,0.07785,0.72056,0.72131,0.47439,0.47662,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42102,SRR5483544,SRX2766893,SRS2150995,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C7 CGATGT L001 R1 001,C7,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC7L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C7 CGATGT L001,C7 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C7_CTTGTA_L001_R1_001.fastq C7_CTTGTA_L001_R2_001.fastq C7_CTTGTA_L002_R1_001.fastq C7_CTTGTA_L002_R2_001.fastq,fastq fastq fastq fastq,1085918450.0,11100560.0,C7 CTTGTA L002 R2 001.fastq,,A:285918868;C:249635769;G:259725006;T:290324468;N:314339,,,,,285918868,249635769,259725006,290324468,314339,SRX2766893,SRS2150995,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93539,0.94346,0.06947,0.06884,0.72421,0.72502,0.4671,0.48382,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42103,SRR5483543,SRX2766892,SRS2150994,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C8 CGATGT L001 R1 001,C8,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC8L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C8 CGATGT L001,C8 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C8_AGTTCC_L001_R1_001.fastq C8_AGTTCC_L001_R2_001.fastq C8_AGTTCC_L002_R1_001.fastq C8_AGTTCC_L002_R2_001.fastq,fastq fastq fastq fastq,1073608497.0,11267084.0,C8 AGTTCC L001 R1 001.fastq,,A:281312906;C:246954741;G:257647783;T:287433153;N:259914,,,,,281312906,246954741,257647783,287433153,259914,SRX2766892,SRS2150994,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93523,0.94416,0.0757,0.07511,0.72868,0.72924,0.45926,0.48524,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42104,SRR5483542,SRX2766891,SRS2150993,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M1 CGATGT L001 R1 001,M1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM1L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M1 CGATGT L001,M1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M1_ATCACG_L001_R1_001.fastq M1_ATCACG_L001_R2_001.fastq M1_ATCACG_L002_R1_001.fastq M1_ATCACG_L002_R2_001.fastq,fastq fastq fastq fastq,1076263104.0,11250362.0,M1 ATCACG L001 R1 001.fastq,,A:283920293;C:247496404;G:257418630;T:287117906;N:309871,,,,,283920293,247496404,257418630,287117906,309871,SRX2766891,SRS2150993,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93089,0.93777,0.07725,0.07679,0.72519,0.7264,0.47634,0.48399,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42105,SRR5483541,SRX2766890,SRS2150992,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M2 CGATGT L001 R1 001,M2,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM2L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M2 CGATGT L001,M2 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M2_TTAGGC_L001_R1_001.fastq M2_TTAGGC_L001_R2_001.fastq M2_TTAGGC_L002_R1_001.fastq M2_TTAGGC_L002_R2_001.fastq,fastq fastq fastq fastq,1044313397.0,10967496.0,M2 TTAGGC L002 R2 001.fastq,,A:276052785;C:238107857;G:247363631;T:282542437;N:246687,,,,,276052785,238107857,247363631,282542437,246687,SRX2766890,SRS2150992,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93066,0.93744,0.08494,0.08454,0.71835,0.72119,0.47424,0.47546,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42106,SRR5483540,SRX2766889,SRS2150991,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M4 CGATGT L001 R1 001,M4,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM4L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M4 CGATGT L001,M4 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M4_ACAGTG_L001_R1_001.fastq M4_ACAGTG_L001_R2_001.fastq M4_ACAGTG_L002_R1_001.fastq M4_ACAGTG_L002_R2_001.fastq,fastq fastq fastq fastq,1040309805.0,10467987.0,M4 ACAGTG L001 R1 001.fastq,,A:274887463;C:239206759;G:246059361;T:279869834;N:286388,,,,,274887463,239206759,246059361,279869834,286388,SRX2766889,SRS2150991,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.92883,0.9367,0.07702,0.07622,0.71723,0.72054,0.47154,0.47398,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42107,SRR5483538,SRX2766888,SRS2150990,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M5 CGATGT L001 R1 001,M5,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM5L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M5 CGATGT L001,M5 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M5_CAGATC_L001_R1_001.fastq M5_CAGATC_L001_R2_001.fastq M5_CAGATC_L002_R1_001.fastq M5_CAGATC_L002_R2_001.fastq,fastq fastq fastq fastq,1042489285.0,10734591.0,M5 CAGATC L002 R1 001.fastq,,A:274701145;C:240814745;G:247900443;T:278809711;N:263241,,,,,274701145,240814745,247900443,278809711,263241,SRX2766888,SRS2150990,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93334,0.94159,0.07462,0.07419,0.7247,0.726,0.46897,0.47065,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42108,SRR5483537,SRX2766887,SRS2150989,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M6 CGATGT L001 R1 001,M6,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM6L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M6 CGATGT L001,M6 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M6_GATCAG_L001_R1_001.fastq M6_GATCAG_L001_R2_001.fastq M6_GATCAG_L002_R1_001.fastq M6_GATCAG_L002_R2_001.fastq,fastq fastq fastq fastq,1031478329.0,10597728.0,M6 GATCAG L001 R1 001.fastq,,A:271373993;C:237256959;G:245402803;T:277169379;N:275195,,,,,271373993,237256959,245402803,277169379,275195,SRX2766887,SRS2150989,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93278,0.93984,0.0768,0.07622,0.72261,0.72494,0.46732,0.48412,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42109,SRR5483536,SRX2766886,SRS2150987,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M7 CGATGT L001 R1 001,M7,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM7L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M7 CGATGT L001,M7 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M7_GGCTAC_L001_R1_001.fastq M7_GGCTAC_L001_R2_001.fastq M7_GGCTAC_L002_R1_001.fastq M7_GGCTAC_L002_R2_001.fastq,fastq fastq fastq fastq,1029672796.0,10581444.0,M7 GGCTAC L001 R2 001.fastq,,A:272134982;C:235882853;G:243458535;T:277945711;N:250715,,,,,272134982,235882853,243458535,277945711,250715,SRX2766886,SRS2150987,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93095,0.93916,0.07906,0.07917,0.72208,0.72376,0.4638,0.47021,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42110,SRR5483535,SRX2766885,SRS2150988,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M8 CGATGT L001 R1 001,M8,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM8L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M8 CGATGT L001,M8 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M8_AGTCAA_L001_R1_001.fastq M8_AGTCAA_L002_R2_001.fastq M8_AGTCAA_L002_R1_001.fastq M8_AGTCAA_L001_R2_001.fastq,fastq fastq fastq fastq,1043646073.0,10637865.0,M8 AGTCAA L002 R2 001.fastq,,A:276074388;C:238813481;G:248854024;T:279639163;N:265017,,,,,276074388,238813481,248854024,279639163,265017,SRX2766885,SRS2150988,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93291,0.94231,0.07997,0.07941,0.73156,0.73594,0.49984,0.50182,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
43749,SRR6047139,SRX3194198,SRS2520599,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control TgMyc TgKras TgMyc&TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism among which the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes in consistent with our observations in lipodomics profiling,,,,,Control,,strain:AB|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin40ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeAB at 6dpf,Control,Control,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_2.fq.gz,fastq fastq,6648275100.0,22160917.0,FCHCKWTBBXX WHZEBleaEAACRAAPEI 20 L1 2.fq.gz,0:150 1:150,A:1742296604;C:1590637599;G:1588423459;T:1726207133;N:710305,150,150,,,1742296604,1590637599,1588423459,1726207133,710305,SRX3194198,SRS2520599,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.91275,0.9117,0.06243,0.06238,0.6743,0.68002,0.48294,0.4832,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43750,SRR6047140,SRX3194197,SRS2520598,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control TgMyc TgKras TgMyc&TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism among which the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes in consistent with our observations in lipodomics profiling,,,,,Myc,,strain:Tgfabp10a:TetON; TRE:Myc|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin41ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeMyc at 6dpf,Myc,Myc,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_2.fq.gz,fastq fastq,6562440900.0,21874803.0,FCHCKWTBBXX WHZEBleaEAABRAAPEI 19 L1 2.fq.gz,0:150 1:150,A:1690373636;C:1597720217;G:1597100889;T:1676557094;N:689064,150,150,,,1690373636,1597720217,1597100889,1676557094,689064,SRX3194197,SRS2520598,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.9112,0.9098,0.05364,0.05314,0.68199,0.68826,0.47506,0.48785,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43751,SRR6047141,SRX3194196,SRS2520597,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control TgMyc TgKras TgMyc&TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism among which the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes in consistent with our observations in lipodomics profiling,,,,,Kras,,strain:Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin42ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras at 6dpf,Kras,Kras,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_2.fq.gz,fastq fastq,6567871200.0,21892904.0,FCHCKWTBBXX WHZEBleaEAADRAAPEI 21 L1 2.fq.gz,0:150 1:150,A:1728249052;C:1564137653;G:1559231198;T:1715565790;N:687507,150,150,,,1728249052,1564137653,1559231198,1715565790,687507,SRX3194196,SRS2520597,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.93087,0.92811,0.06342,0.06328,0.66941,0.67493,0.47581,0.47601,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43752,SRR6047142,SRX3194195,SRS2520596,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control TgMyc TgKras TgMyc&TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism among which the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes in consistent with our observations in lipodomics profiling,,,,,Kras&Myc,,strain:Tgfabp10a:TetON; TRE:Myc&Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin43ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras&Myc at 6dpf,Kras&Myc,Kras&Myc,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_2.fq.gz,fastq fastq,6464892900.0,21549643.0,FCHCKWTBBXX WHZEBleaEAAARAAPEI 18 L1 2.fq.gz,0:150 1:150,A:1676039250;C:1565410813;G:1564742343;T:1658019117;N:681377,150,150,,,1676039250,1565410813,1564742343,1658019117,681377,SRX3194195,SRS2520596,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.8919,0.88916,0.05486,0.05403,0.67882,0.68505,0.49625,0.49784,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
49393,SRR7896793,SRX4734232,SRS3816349,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,homozygous mutant,,strain:tnnt2a / |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of tnnt2a homozygous mutant zebrafish post Dox induction,homozygous mutant,homozygous mutant,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,mutant_L1_1.fq.gz mutant_L1_2.fq.gz,fastq fastq,6615980100.0,22053267.0,mutant L1 2.fq.gz,0:150 1:150,A:1714364351;C:1596934293;G:1606676062;T:1697294755;N:710639,150,150,,,1714364351,1596934293,1606676062,1697294755,710639,SRX4734232,SRS3816349,,,Children's hospital of Fudan University,2,0.88229,0.88599,0.05373,0.05345,0.67042,0.67259,0.45764,0.46314,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49394,SRR7896794,SRX4734231,SRS3816348,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,non homozygous mutant,,strain:tnnt2a+/ |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of non tnnt2a homozygous mutant zebrafish post Dox induction,non homozygous mutant,non homozygous mutant,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,non mutant_L1_1.fq.gz non mutant_L1_2.fq.gz,fastq fastq,6561723600.0,21872412.0,non mutant L1 2.fq.gz,0:150 1:150,A:1689788269;C:1592764528;G:1601424044;T:1677002898;N:743861,150,150,,,1689788269,1592764528,1601424044,1677002898,743861,SRX4734231,SRS3816348,,,Children's hospital of Fudan University,2,0.8991,0.90343,0.05565,0.05598,0.66752,0.66929,0.4567,0.46188,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49395,SRR7896795,SRX4734230,SRS3816347,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,transgene homozygous mutant,,strain:Tgcmlc2:TetON; tnnt2a p2A mKate2&tnnt2a / |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of transgene tnnt2a homozygous mutant zebrafish post Dox induction,transgene homozygous mutant,transgene homozygous mutant,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,transgene mutant_L1_1.fq.gz transgene mutant_L1_2.fq.gz,fastq fastq,6496976700.0,21656589.0,transgene mutant L1 2.fq.gz,,,,,,,,,,,,SRX4734230,SRS3816347,,,Children's hospital of Fudan University,2,0.9041,0.8968,0.06697,0.06595,0.66789,0.66787,0.45258,0.45688,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49396,SRR7896796,SRX4734229,SRS3816346,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,non transgene homozyous mutant,,strain:Tgcmlc2:TetON; tnnt2a p2A mKate2&tnnt2a+/ |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of non transgene tnnt2a homozygous mutant zebrafish post Dox induction,non transgene homozyous mutant,non transgene homozyous mutant,In our project we sequence 4 samples use Illumina Hiseq platform and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,transgene non mutant_L1_1.fq.gz transgene non mutant_L1_2.fq.gz,fastq fastq,6541491300.0,21804971.0,transgene non mutant L1 1.fq.gz,0:150 1:150,A:1689774214;C:1582775230;G:1591564227;T:1676650852;N:726777,150,150,,,1689774214,1582775230,1591564227,1676650852,726777,SRX4734229,SRS3816346,,,Children's hospital of Fudan University,2,0.89333,0.89894,0.05656,0.05595,0.66665,0.66888,0.46433,0.46204,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49738,SRR8009939,SRX4840767,SRS3905926,SRP165180,PRJNA495704,Danio rerio strain:Tubingen Transcriptome or Gene expression,PRJNA495704,Other,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,,,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,Danio rerio SMAR1 Morpholino mediated knockdown,SMAR1 Morpholino,,strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of SMAR1 Morpholino injected Danio rerio Embryo,TB1 MO 1,TB1 MO 1,Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 500,,SRP165180,,,,,4848491136.0,31897968.0,TB1 MO 1 R2.fastq.gz,0:76 1:76,A:1279455755;C:1177863867;G:1126629683;T:1263248208;N:1293623,76,76,,,1279455755,1177863867,1126629683,1263248208,1293623,SRX4840767,SRS3905926,SRA792799,Indian Institute of Chemical Biology|Chromatin and Disease Biology,"Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad",2,0.94763,0.94494,0.08466,0.0847,0.68477,0.68941,0.45531,0.46264,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2018-10-11,Hatching,Embryo,Whole Organism,All anatomical structures
49739,SRR8009940,SRX4840766,SRS3905926,SRP165180,PRJNA495704,Danio rerio strain:Tubingen Transcriptome or Gene expression,PRJNA495704,Other,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,,,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,Danio rerio SMAR1 Morpholino mediated knockdown,SMAR1 Morpholino,,strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of SMAR1 Morpholino injected Danio rerio Embryo,TB1 MO 2,TB1 MO 2,Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 500,,SRP165180,,,,,5229981040.0,34407770.0,TB1 MO 2 R2.fastq.gz,0:76 1:76,A:1375946341;C:1255628851;G:1212656512;T:1382649755;N:3099581,76,76,,,1375946341,1255628851,1212656512,1382649755,3099581,SRX4840766,SRS3905926,SRA792799,Indian Institute of Chemical Biology|Chromatin and Disease Biology,"Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad",2,0.95547,0.95355,0.08995,0.08948,0.6799,0.68365,0.46004,0.46022,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2018-10-11,Hatching,Embryo,Whole Organism,All anatomical structures
49740,SRR8009941,SRX4840765,SRS3905926,SRP165180,PRJNA495704,Danio rerio strain:Tubingen Transcriptome or Gene expression,PRJNA495704,Other,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,,,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,Danio rerio SMAR1 Morpholino mediated knockdown,SMAR1 Morpholino,,strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Control Morpholino injected Danio rerio Embryo,CTRL MO 1,CTRL MO 1,Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 500,,SRP165180,,,,,5396333184.0,35502192.0,CTRL MO 1 R2.fastq.gz,0:76 1:76,A:1423972325;C:1290764003;G:1246450472;T:1431965693;N:3180691,76,76,,,1423972325,1290764003,1246450472,1431965693,3180691,SRX4840765,SRS3905926,SRA792799,Indian Institute of Chemical Biology|Chromatin and Disease Biology,"Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad",2,0.95835,0.95512,0.09447,0.09425,0.68038,0.68416,0.4619,0.45317,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2018-10-11,Hatching,Embryo,Whole Organism,All anatomical structures
49741,SRR8009942,SRX4840764,SRS3905926,SRP165180,PRJNA495704,Danio rerio strain:Tubingen Transcriptome or Gene expression,PRJNA495704,Other,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,,,Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.,Danio rerio SMAR1 Morpholino mediated knockdown,SMAR1 Morpholino,,strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Control Morpholino injected Danio rerio Embryo,CTRL M0 2,CTRL M0 2,Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 500,,SRP165180,,,,,4661867664.0,30670182.0,CTRL MO 2 R1.fastq.gz,0:76 1:76,A:1224151482;C:1123655254;G:1082094210;T:1229195581;N:2771137,76,76,,,1224151482,1123655254,1082094210,1229195581,2771137,SRX4840764,SRS3905926,SRA792799,Indian Institute of Chemical Biology|Chromatin and Disease Biology,"Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad",2,0.95816,0.95561,0.08583,0.08611,0.67829,0.68345,0.46037,0.45464,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2018-10-11,Hatching,Embryo,Whole Organism,All anatomical structures
51812,SRR8862072,SRX5649486,SRS4594851,SRP191202,PRJNA531242,Zebrafish Otolith Biomineralization Requires Polyketide Synthase,PRJNA531242,Other,RNA seq analysis of nco no content zebrafish embryos at 24 hpf,,,,,Wild type,,strain:AB|age:24hpf|sex:pooled male and female|tissue:Whole embryo lysate|genotype:WT|phenotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 24hpf Danio rerio WT,WT,WT,Expression profiling by high throughput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP191202,,,WT_accepted_hits.bam,bam,4678276912.0,46627860.0,WT accepted hits.bam,0:100.33,A:1220754988;C:1121942916;G:1099337627;T:1236237181;N:4200,100,,,,1220754988,1121942916,1099337627,1236237181,4200,SRX5649486,SRS4594851,SRA870334,Creighton University|Biomedical Sciences,Creighton University,1,0.99199,,0.07435,,0.69587,,0.47078,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-04-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
51813,SRR8862073,SRX5649485,SRS4594850,SRP191202,PRJNA531242,Zebrafish Otolith Biomineralization Requires Polyketide Synthase,PRJNA531242,Other,RNA seq analysis of nco no content zebrafish embryos at 24 hpf,,,,,nco mutant,,strain:AB|age:24hpf|sex:pooled male and female|tissue:Whole embryo lysate|genotype:nco|phenotype:otolith agenesis|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 24hpf Danio rerio nco,nco,nco,Expression profiling by high throughput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP191202,,,MUT_accepted_hits.bam,bam,4123578221.0,41065807.0,MUT accepted hits.bam,0:100.41,A:1067146358;C:996426621;G:980020305;T:1079981310;N:3627,100,,,,1067146358,996426621,980020305,1079981310,3627,SRX5649485,SRS4594850,SRA870334,Creighton University|Biomedical Sciences,Creighton University,1,0.9923,,0.06787,,0.69901,,0.46967,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-04-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
55843,SRR10862985,SRX7533084,SRS5972252,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 2dpf rep3,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 2dpf,wt PGCs 2dpf rep3 totalRNA,wt PGCs 2dpf rep3 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,03072018-wt_PGCs_2dpf_rep3_totalRNA.R1.fastq.gz 03072018-wt_PGCs_2dpf_rep3_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep3_totalRNA.R1.fastq.gz 14022018-wt_PGCs_2dpf_rep3_totalRNA.R2.fastq.gz,fastq fastq fastq fastq,3149016822.0,21605375.0,03072018 wt PGCs 2dpf rep3 totalRNA.R1.fastq.gz,0:72.88 1:72.88,A:882764631;C:692736186;G:686376514;T:886384367;N:755124,72,72,,,882764631,692736186,686376514,886384367,755124,SRX7533084,SRS5972252,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.86749,0.86961,0.31266,0.31842,0.66807,0.67359,0.63363,0.63454,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Hatching,Embryo,Whole Organism,All anatomical structures
55844,SRR10862986,SRX7533083,SRS5972244,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 2dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 2dpf,wt PGCs 2dpf rep2 totalRNA,wt PGCs 2dpf rep2 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,14022018-wt_PGCs_2dpf_rep2_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep2_totalRNA.R1.fastq.gz 09072018-wt_PGCs_2dpf_rep2_totalRNA.R2.fastq.gz 09072018-wt_PGCs_2dpf_rep2_totalRNA.R1.fastq.gz,fastq fastq fastq fastq,3023614944.0,20997326.0,09072018 wt PGCs 2dpf rep2 totalRNA.R1.fastq.gz,0:72 1:72,A:856012866;C:645772980;G:664213827;T:856875833;N:739438,72,72,,,856012866,645772980,664213827,856875833,739438,SRX7533083,SRS5972244,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.89654,0.88678,0.30038,0.29916,0.66539,0.67322,0.65371,0.65661,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Hatching,Embryo,Whole Organism,All anatomical structures
55845,SRR10862987,SRX7533082,SRS5972269,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 2dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 2dpf,wt PGCs 2dpf rep1 totalRNA,wt PGCs 2dpf rep1 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,14022018-wt_PGCs_2dpf_rep1_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep1_totalRNA.R1.fastq.gz 03072018-wt_PGCs_2dpf_rep1_totalRNA.R2.fastq.gz 03072018-wt_PGCs_2dpf_rep1_totalRNA.R1.fastq.gz,fastq fastq fastq fastq,3143598780.0,21555803.0,03072018 wt PGCs 2dpf rep1 totalRNA.R1.fastq.gz,0:72.92 1:72.92,A:889549293;C:680890464;G:675921445;T:896506040;N:731538,72,72,,,889549293,680890464,675921445,896506040,731538,SRX7533082,SRS5972269,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.87081,0.87619,0.35764,0.36603,0.69112,0.69534,0.61958,0.50175,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Hatching,Embryo,Whole Organism,All anatomical structures
55846,SRR10862988,SRX7533081,SRS5972268,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 1dpf rep3,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf rep3 totalRNA,wt PGCs 1dpf rep3 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,09072018-wt_PGCs_1dpf_rep3_totalRNA.R1.fastq.gz 14022018-wt_PGCs_1dpf_rep3_totalRNA.R2.fastq.gz 14022018-wt_PGCs_1dpf_rep3_totalRNA.R1.fastq.gz 09072018-wt_PGCs_1dpf_rep3_totalRNA.R2.fastq.gz,fastq fastq fastq fastq,3082887936.0,21408944.0,09072018 wt PGCs 1dpf rep3 totalRNA.R1.fastq.gz,0:72 1:72,A:855717326;C:671894681;G:694821062;T:859704799;N:750068,72,72,,,855717326,671894681,694821062,859704799,750068,SRX7533081,SRS5972268,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.91419,0.90389,0.26055,0.25953,0.68331,0.68968,0.69151,0.69054,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures