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
32,DRR408242,DRX393848,DRS407006,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 3,zebrafish adult gut replicate 3,SAMD00529462,,sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529462,DRX393848,AR019 gut 6 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529462,,,,3546347364.0,28145614.0,DRR408242,0:126 1:0,A:919466631;C:829424335;G:818581155;T:978810217;N:65026,126,0,,,919466631,829424335,818581155,978810217,65026,DRX393848,DRS407006,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
33,DRR408241,DRX393847,DRS407005,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 2,zebrafish adult gut replicate 2,SAMD00529461,,sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529461,DRX393847,AR006 gut 4 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529461,,,,3671973648.0,29142648.0,DRR408241,0:126 1:0,A:942167543;C:859431290;G:852661772;T:1017643011;N:70032,126,0,,,942167543,859431290,852661772,1017643011,70032,DRX393847,DRS407005,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
34,DRR408240,DRX393846,DRS407004,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 1,zebrafish adult gut replicate 1,SAMD00529460,,sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529460,DRX393846,AR004 gut 2 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529460,,,,3480523704.0,27623204.0,DRR408240,0:126 1:0,A:898051986;C:827557593;G:816541244;T:938307607;N:65274,126,0,,,898051986,827557593,816541244,938307607,65274,DRX393846,DRS407004,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
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
9842,ERR4029259,ERX4030575,ERS4514128,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 4,SAMEA6786449,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786449|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 4 p,Sample 4 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz,fastq fastq,4354809436.0,29071030.0,E MTAB 8958:FB4 S41 R,0:74.90 1:74.90,A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114,74,74,,,1140431810,1005396495,1008528915,1171220102,29232114,ERX4030575,ERS4514128,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91143,0.91076,0.10123,0.09941,0.68235,0.68452,0.48713,0.48998,76,74,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9843,ERR4029258,ERX4030574,ERS4514127,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 3,SAMEA6786448,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786448|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 3 p,Sample 3 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz,fastq fastq,3973860397.0,26559713.0,E MTAB 8958:FB3 S40 R,0:74.80 1:74.82,A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766,74,74,,,1038749031,917944667,920080717,1066160216,30925766,ERX4030574,ERS4514127,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91065,0.90981,0.10133,0.09911,0.68789,0.68945,0.47182,0.49996,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9844,ERR4029257,ERX4030573,ERS4514126,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 2,SAMEA6786447,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786447|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 2 p,Sample 2 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz,fastq fastq,4135184845.0,27517010.0,E MTAB 8958:FB2 S39 R,0:75.15 1:75.13,A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419,75,75,,,1084253902,962303819,961163738,1111949967,15513419,ERX4030573,ERS4514126,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91098,0.91057,0.09468,0.09311,0.68095,0.68282,0.49982,0.50146,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9845,ERR4029256,ERX4030572,ERS4514125,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 1,SAMEA6786446,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786446|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 1 p,Sample 1 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 06 17,FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq,fastq fastq,4651073045.0,31021879.0,E MTAB 8958:FB1 S38 R,0:74.96 1:74.97,A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744,74,74,,,1225305023,1072643957,1069905162,1255950159,27268744,ERX4030572,ERS4514125,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91441,0.91282,0.10095,0.09913,0.686,0.68745,0.49433,0.5047,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9846,ERR4029255,ERX4030571,ERS4514124,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 16,SAMEA6786445,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786445|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 16|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 16|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 16 p,Sample 16 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz,fastq fastq,5961540086.0,39717871.0,E MTAB 8958:FB4 S20 R,0:75.07 1:75.03,A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639,75,75,,,1565483441,1390303898,1372759826,1611361282,21631639,ERX4030571,ERS4514124,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90959,0.90989,0.0925,0.09172,0.68787,0.68929,0.49093,0.49057,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9847,ERR4029254,ERX4030570,ERS4514123,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 15,SAMEA6786444,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786444|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 15|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 15|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 15 p,Sample 15 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz,fastq fastq,6835575760.0,45515064.0,E MTAB 8958:FB3 S19 R,0:75.11 1:75.07,A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710,75,75,,,1802176562,1589590146,1564279107,1858606235,20923710,ERX4030570,ERS4514123,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90945,0.91123,0.09519,0.09378,0.67963,0.67961,0.49246,0.49476,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9848,ERR4029253,ERX4030569,ERS4514122,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 14,SAMEA6786443,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 14 p,Sample 14 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz,fastq fastq,5789923311.0,38517674.0,E MTAB 8958:FB2 S18 R,0:75.18 1:75.14,A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457,75,75,,,1520250885,1354960735,1336204150,1565011084,13496457,ERX4030569,ERS4514122,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91863,0.91917,0.08923,0.08753,0.68848,0.68883,0.5042,0.50799,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9849,ERR4029252,ERX4030568,ERS4514121,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 13,SAMEA6786442,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786442|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 13|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 13|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 13 p,Sample 13 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz,fastq fastq,6951804793.0,46295025.0,E MTAB 8958:FB1 S17 R,0:75.10 1:75.06,A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094,75,75,,,1827618209,1618955946,1595802123,1884739421,24689094,ERX4030568,ERS4514121,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90991,0.90972,0.09297,0.09193,0.68284,0.68392,0.49878,0.5017,74,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9850,ERR4029251,ERX4030567,ERS4514120,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 20,SAMEA6786441,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786441|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 20|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 20|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 20 p,Sample 20 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz,fastq fastq,9629684100.0,64667395.0,E MTAB 8958:FB4 S44 R,0:74.47 1:74.44,A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676,74,74,,,2552333346,2176006333,2180111416,2614191329,107041676,ERX4030567,ERS4514120,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90795,0.90756,0.10044,0.09789,0.6888,0.69256,0.50043,0.4932,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9851,ERR4029250,ERX4030566,ERS4514119,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 19,SAMEA6786440,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786440|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 19|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 19|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 19 p,Sample 19 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz,fastq fastq,11268744444.0,75088756.0,E MTAB 8958:FB3 S43 R,0:75.06 1:75.01,A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891,75,75,,,2983863814,2608268633,2555098938,3072413168,49099891,ERX4030566,ERS4514119,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9107,0.91089,0.09522,0.09428,0.69187,0.69266,0.49302,0.49463,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9852,ERR4029249,ERX4030565,ERS4514118,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 18,SAMEA6786439,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786439|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 18|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 18|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 18 p,Sample 18 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz,fastq fastq,10434072067.0,69530304.0,E MTAB 8958:FB2 S42 R,0:75.06 1:75.01,A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042,75,75,,,2749500618,2426208950,2375421255,2834879202,48062042,ERX4030565,ERS4514118,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9084,0.90779,0.0926,0.0917,0.68809,0.68864,0.49817,0.49902,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9853,ERR4029248,ERX4030564,ERS4514117,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 17,SAMEA6786438,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786438|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 17|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 17|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 17 p,Sample 17 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz,fastq fastq,12125040750.0,80781224.0,E MTAB 8958:FB1 S41 R,0:75.08 1:75.02,A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600,75,75,,,3129480022,2890038396,2819859086,3233228646,52434600,ERX4030564,ERS4514117,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91384,0.91301,0.10967,0.10615,0.69006,0.69041,0.51643,0.51985,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9854,ERR4029247,ERX4030563,ERS4514116,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 8,SAMEA6786437,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786437|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 8|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 8 p,Sample 8 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz,fastq fastq,4223131851.0,28165494.0,E MTAB 8958:FB12 S49 R,0:74.95 1:74.99,A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146,74,74,,,1121514270,962554300,967294488,1146544647,25224146,ERX4030563,ERS4514116,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91639,0.91413,0.10604,0.10326,0.68162,0.68458,0.49921,0.50172,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9855,ERR4029246,ERX4030562,ERS4514115,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 7,SAMEA6786436,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786436|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 7|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 7 p,Sample 7 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz,fastq fastq,4670407305.0,31054128.0,E MTAB 8958:FB11 S48 R,0:75.20 1:75.19,A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954,75,75,,,1234494738,1078360233,1084251975,1258088405,15211954,ERX4030562,ERS4514115,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92228,0.92038,0.09418,0.09222,0.68674,0.68862,0.48948,0.48842,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9856,ERR4029245,ERX4030561,ERS4514114,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 6,SAMEA6786435,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786435|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 6|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 6 p,Sample 6 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz,fastq fastq,3970723047.0,26597167.0,E MTAB 8958:FB10 S47 R,0:74.63 1:74.66,A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680,74,74,,,1037861230,915437247,922979694,1056625196,37819680,ERX4030561,ERS4514114,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92474,0.92246,0.0934,0.0916,0.69106,0.69384,0.49058,0.48154,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9857,ERR4029244,ERX4030560,ERS4514113,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 5,SAMEA6786434,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786434|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 5 p,Sample 5 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz,fastq fastq,4267946165.0,28455064.0,E MTAB 8958:FB9 S46 R,0:75.00 1:74.99,A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111,75,74,,,1108310330,999732020,987857724,1148193980,23852111,ERX4030560,ERS4514113,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9223,0.91737,0.09304,0.09006,0.69063,0.6929,0.48978,0.49675,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9858,ERR4029243,ERX4030559,ERS4514112,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 9,SAMEA6786433,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786433|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 9|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 9 p,Sample 9 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz,fastq fastq,3847723303.0,25764874.0,E MTAB 8958:FB17 S54 R,0:74.65 1:74.69,A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451,74,74,,,1009950686,883047473,885821368,1035313325,33590451,ERX4030559,ERS4514112,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91088,0.90785,0.09899,0.09623,0.68822,0.69055,0.48686,0.49337,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9859,ERR4029242,ERX4030558,ERS4514111,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 12,SAMEA6786432,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786432|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 12|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 12 p,Sample 12 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz,fastq fastq,4534822065.0,30209756.0,E MTAB 8958:FB20 S57 R,0:75.06 1:75.06,A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622,75,75,,,1181838544,1056097162,1066594521,1207484216,22807622,ERX4030558,ERS4514111,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91577,0.91513,0.09598,0.09473,0.68931,0.69132,0.49181,0.49786,74,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9860,ERR4029241,ERX4030557,ERS4514110,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 11,SAMEA6786431,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786431|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 11|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 11|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 11 p,Sample 11 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz,fastq fastq,5070571422.0,33987501.0,E MTAB 8958:FB19 S56 R,0:74.58 1:74.61,A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944,74,74,,,1327496786,1163563377,1162870630,1365191685,51448944,ERX4030557,ERS4514110,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91091,0.91003,0.09944,0.09748,0.68745,0.69016,0.49706,0.49287,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9861,ERR4029240,ERX4030556,ERS4514109,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 10,SAMEA6786430,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786430|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 10|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 10 p,Sample 10 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz,fastq fastq,4411576023.0,29389076.0,E MTAB 8958:FB18 S55 R,0:75.05 1:75.06,A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829,75,75,,,1153821133,1024593137,1029312154,1181989770,21859829,ERX4030556,ERS4514109,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90933,0.90999,0.09581,0.09404,0.68917,0.69199,0.49527,0.49791,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
15614,ERR13109732,ERX12481366,ERS19896183,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT young,SAMEA115618603,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT young p,WT young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_young_S16_L002_I1_001.fastq.gz WT_young_S16_L002_R1_001.fastq.gz WT_young_S16_L002_R2_001.fastq.gz,fastq fastq fastq,11547230144.0,90923072.0,E MTAB 14075:WT young S16 L002,0:8 1:28 2:91,A:2298760158;C:1887715706;G:1977278606;T:2109839457;N:405625,8,28,91,,2298760158,1887715706,1977278606,2109839457,405625,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15615,ERR13109737,ERX12481366,ERS19896183,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT young,SAMEA115618603,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT young p,WT young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_young_run2_S10_L001_I1_001.fastq.gz WT_young_run2_S10_L001_R1_001.fastq.gz WT_young_run2_S10_L001_R2_001.fastq.gz,fastq fastq fastq,6300899375.0,50407195.0,E MTAB 14075:WT young run2 S10 L001,0:8 1:28 2:89,A:1243074350;C:1030040216;G:1079454879;T:1133663108;N:7802,8,28,89,,1243074350,1030040216,1079454879,1133663108,7802,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15616,ERR13109733,ERX12481366,ERS19896183,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT young,SAMEA115618603,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT young p,WT young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_young_run2_S10_L002_I1_001.fastq.gz WT_young_run2_S10_L002_R1_001.fastq.gz WT_young_run2_S10_L002_R2_001.fastq.gz,fastq fastq fastq,6323980500.0,50591844.0,E MTAB 14075:WT young run2 S10 L002,0:8 1:28 2:89,A:1248024810;C:1032976792;G:1082805513;T:1138855823;N:11178,8,28,89,,1248024810,1032976792,1082805513,1138855823,11178,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15617,ERR13109728,ERX12481366,ERS19896183,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT young,SAMEA115618603,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT young p,WT young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_young_S16_L001_I1_001.fastq.gz WT_young_S16_L001_R1_001.fastq.gz WT_young_S16_L001_R2_001.fastq.gz,fastq fastq fastq,9395132467.0,73977421.0,E MTAB 14075:WT young S16 L001,0:8 1:28 2:91,A:1870197969;C:1535772308;G:1609450193;T:1716224344;N:300497,8,28,91,,1870197969,1535772308,1609450193,1716224344,300497,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15618,ERR13109727,ERX12481365,ERS19896182,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT aged,SAMEA115618602,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT aged p,WT aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_aged_S15_L001_I1_001.fastq.gz WT_aged_S15_L001_R1_001.fastq.gz WT_aged_S15_L001_R2_001.fastq.gz,fastq fastq fastq,3224055528.0,25386264.0,E MTAB 14075:WT aged S15 L001,0:8 1:28 2:91,A:632762441;C:548488749;G:552881879;T:575917355;N:99600,8,28,91,,632762441,548488749,552881879,575917355,99600,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15619,ERR13109729,ERX12481365,ERS19896182,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT aged,SAMEA115618602,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT aged p,WT aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_aged_S15_L002_I1_001.fastq.gz WT_aged_S15_L002_R1_001.fastq.gz WT_aged_S15_L002_R2_001.fastq.gz,fastq fastq fastq,4178136043.0,32898709.0,E MTAB 14075:WT aged S15 L002,0:8 1:28 2:91,A:820476445;C:710661272;G:715891121;T:746611018;N:142663,8,28,91,,820476445,710661272,715891121,746611018,142663,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15620,ERR13109731,ERX12481365,ERS19896182,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT aged,SAMEA115618602,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT aged p,WT aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_aged_run2_S13_L002_I1_001.fastq.gz WT_aged_run2_S13_L002_R1_001.fastq.gz WT_aged_run2_S13_L002_R2_001.fastq.gz,fastq fastq fastq,11315635500.0,90525084.0,E MTAB 14075:WT aged run2 S13 L002,0:8 1:28 2:89,A:2205965370;C:1918372621;G:1938090305;T:1994285205;N:18975,8,28,89,,2205965370,1918372621,1938090305,1994285205,18975,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15621,ERR13109734,ERX12481365,ERS19896182,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,WT aged,SAMEA115618602,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:WT aged p,WT aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,WT_aged_run2_S13_L001_I1_001.fastq.gz WT_aged_run2_S13_L001_R1_001.fastq.gz WT_aged_run2_S13_L001_R2_001.fastq.gz,fastq fastq fastq,11297009750.0,90376078.0,E MTAB 14075:WT aged run2 S13 L001,0:8 1:28 2:89,A:2201626807;C:1916371507;G:1936001373;T:1989457619;N:13636,8,28,89,,2201626807,1916371507,1936001373,1989457619,13636,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15622,ERR13109730,ERX12481363,ERS19896180,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het aged,SAMEA115618600,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het aged p,Het aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_aged_run2_S14_L002_I1_001.fastq.gz Het_aged_run2_S14_L002_R1_001.fastq.gz Het_aged_run2_S14_L002_R2_001.fastq.gz,fastq fastq fastq,4755473375.0,38043787.0,E MTAB 14075:Het aged run2 S14 L002,0:8 1:28 2:89,A:924628155;C:804435427;G:826904786;T:829920091;N:8584,8,28,89,,924628155,804435427,826904786,829920091,8584,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15623,ERR13109738,ERX12481363,ERS19896180,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het aged,SAMEA115618600,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het aged p,Het aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_aged_run2_S14_L001_I1_001.fastq.gz Het_aged_run2_S14_L001_R1_001.fastq.gz Het_aged_run2_S14_L001_R2_001.fastq.gz,fastq fastq fastq,4757077375.0,38056619.0,E MTAB 14075:Het aged run2 S14 L001,0:8 1:28 2:89,A:924804478;C:805146986;G:827570549;T:829511132;N:5946,8,28,89,,924804478,805146986,827570549,829511132,5946,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15624,ERR13109725,ERX12481363,ERS19896180,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het aged,SAMEA115618600,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het aged p,Het aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_aged_S13_L001_I1_001.fastq.gz Het_aged_S13_L001_R1_001.fastq.gz Het_aged_S13_L001_R2_001.fastq.gz,fastq fastq fastq,2031302643.0,15994509.0,E MTAB 14075:Het aged S13 L001,0:8 1:28 2:91,A:398278357;C:344264985;G:353424298;T:359473296;N:59383,8,28,91,,398278357,344264985,353424298,359473296,59383,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15625,ERR13109739,ERX12481363,ERS19896180,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het aged,SAMEA115618600,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het aged p,Het aged p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_aged_S13_L002_I1_001.fastq.gz Het_aged_S13_L002_R1_001.fastq.gz Het_aged_S13_L002_R2_001.fastq.gz,fastq fastq fastq,2430576292.0,19138396.0,E MTAB 14075:Het aged S13 L002,0:8 1:28 2:91,A:476457271;C:411953563;G:422659830;T:430445714;N:77658,8,28,91,,476457271,411953563,422659830,430445714,77658,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15626,ERR13109736,ERX12481364,ERS19896181,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het young,SAMEA115618601,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het young p,Het young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_young_S14_L001_I1_001.fastq.gz Het_young_S14_L001_R1_001.fastq.gz Het_young_S14_L001_R2_001.fastq.gz,fastq fastq fastq,7202197051.0,56710213.0,E MTAB 14075:Het young S14 L001,0:8 1:28 2:91,A:1452033851;C:1164601809;G:1229900451;T:1313862644;N:230628,8,28,91,,1452033851,1164601809,1229900451,1313862644,230628,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15627,ERR13109740,ERX12481364,ERS19896181,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het young,SAMEA115618601,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het young p,Het young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_young_run2_S11_L001_I1_001.fastq.gz Het_young_run2_S11_L001_R1_001.fastq.gz Het_young_run2_S11_L001_R2_001.fastq.gz,fastq fastq fastq,3012722750.0,24101782.0,E MTAB 14075:Het young run2 S11 L001,0:8 1:28 2:89,A:601664996;C:487380557;G:514748426;T:541261211;N:3408,8,28,89,,601664996,487380557,514748426,541261211,3408,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15628,ERR13109735,ERX12481364,ERS19896181,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het young,SAMEA115618601,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het young p,Het young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_young_run2_S11_L002_I1_001.fastq.gz Het_young_run2_S11_L002_R1_001.fastq.gz Het_young_run2_S11_L002_R2_001.fastq.gz,fastq fastq fastq,3017568125.0,24140545.0,E MTAB 14075:Het young run2 S11 L002,0:8 1:28 2:89,A:602793366;C:487819335;G:515271935;T:542618728;N:5141,8,28,89,,602793366,487819335,515271935,542618728,5141,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15629,ERR13109726,ERX12481364,ERS19896181,ERP160330,PRJEB75769,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E-MTAB-14075,Transcriptome Analysis,The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,,Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,Het young,SAMEA115618601,Department of Hematology cancer institute ErasmusMC,ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO,,,,,,,,,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,E MTAB 14075:Het young p,Het young p,Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP160330,Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish,ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05,Het_young_S14_L002_I1_001.fastq.gz Het_young_S14_L002_R1_001.fastq.gz Het_young_S14_L002_R2_001.fastq.gz,fastq fastq fastq,8707482077.0,68562851.0,E MTAB 14075:Het young S14 L002,0:8 1:28 2:91,A:1755361511;C:1408255848;G:1486295783;T:1588996810;N:309489,8,28,91,,1755361511,1408255848,1486295783,1588996810,309489,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
25135,SRR25649156,SRX21375305,SRS18618397,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X8,18689X8,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X8_R1.fastq.gz 18689X8_R2.fastq.gz,fastq fastq,8163984120.0,27033060.0,18689X8 R1.fastq.gz,0:151 1:151,A:1900143724;C:2183735704;G:2147710753;T:1932229591;N:164348,151,151,,,1900143724,2183735704,2147710753,1932229591,164348,SRX21375305,SRS18618397,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89288,0.89479,0.20193,0.20116,0.79072,0.79352,0.57246,0.56409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25136,SRR25649157,SRX21375304,SRS18618396,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X15,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X15,19629X15,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X15_R2.fastq.gz 19629X15_R1.fastq.gz,fastq fastq,10277997106.0,34033103.0,19629X15 R1.fastq.gz,0:151 1:151,A:2798108841;C:2341310321;G:2438634645;T:2699729301;N:213998,151,151,,,2798108841,2341310321,2438634645,2699729301,213998,SRX21375304,SRS18618396,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90655,0.90714,0.18082,0.18027,0.72803,0.72953,0.45722,0.45335,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25137,SRR25649158,SRX21375303,SRS18618395,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X14,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 3|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X14,19629X14,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X14_R1.fastq.gz 19629X14_R2.fastq.gz,fastq fastq,10921707086.0,36164593.0,19629X14 R1.fastq.gz,0:151 1:151,A:2969229092;C:2484790148;G:2595052715;T:2872407360;N:227771,151,151,,,2969229092,2484790148,2595052715,2872407360,227771,SRX21375303,SRS18618395,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90015,0.90211,0.19548,0.19546,0.72997,0.73131,0.53978,0.54998,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25138,SRR25649159,SRX21375302,SRS18618394,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X13,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X13,19629X13,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X13_R1.fastq.gz 19629X13_R2.fastq.gz,fastq fastq,10019262230.0,33176365.0,19629X13 R1.fastq.gz,0:151 1:151,A:2732766602;C:2270429150;G:2391166434;T:2624690350;N:209694,151,151,,,2732766602,2270429150,2391166434,2624690350,209694,SRX21375302,SRS18618394,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90381,0.90536,0.18425,0.18388,0.72681,0.72936,0.48627,0.49398,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25139,SRR25649160,SRX21375301,SRS18618393,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X12,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X12,19629X12,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X12_R1.fastq.gz 19629X12_R2.fastq.gz,fastq fastq,11078632326.0,36684213.0,19629X12 R1.fastq.gz,0:151 1:151,A:2995473302;C:2550446088;G:2653594689;T:2878887522;N:230725,151,151,,,2995473302,2550446088,2653594689,2878887522,230725,SRX21375301,SRS18618393,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91101,0.91121,0.16145,0.16142,0.70274,0.70498,0.47852,0.48788,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25140,SRR25649161,SRX21375300,SRS18618392,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X11,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X11,19629X11,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X11_R1.fastq.gz 19629X11_R2.fastq.gz,fastq fastq,10957183630.0,36282065.0,19629X11 R1.fastq.gz,0:151 1:151,A:2987773085;C:2485587980;G:2603747193;T:2879845340;N:230032,151,151,,,2987773085,2485587980,2603747193,2879845340,230032,SRX21375300,SRS18618392,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91198,0.91301,0.20992,0.20926,0.73044,0.73316,0.44301,0.43596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25141,SRR25649162,SRX21375299,SRS18618390,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X10,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X10,19629X10,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X10_R1.fastq.gz 19629X10_R2.fastq.gz,fastq fastq,9549065142.0,31619421.0,19629X10 R1.fastq.gz,0:151 1:151,A:2603092155;C:2167963952;G:2264536965;T:2513273275;N:198795,151,151,,,2603092155,2167963952,2264536965,2513273275,198795,SRX21375299,SRS18618390,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.92549,0.92615,0.16176,0.15925,0.7683,0.76926,0.3093,0.30927,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25142,SRR25649163,SRX21375298,SRS18618391,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X4,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X4,18843X4,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X4_R1.fastq.gz 18843X4_R2.fastq.gz,fastq fastq,7982656072.0,26432636.0,18843X4 R1.fastq.gz,0:151 1:151,A:2135066517;C:1863182314;G:1988885981;T:1995395692;N:125568,151,151,,,2135066517,1863182314,1988885981,1995395692,125568,SRX21375298,SRS18618391,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.86144,0.85982,0.30956,0.30838,0.70731,0.71356,0.48481,0.48054,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25143,SRR25649164,SRX21375297,SRS18618389,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X5,18843X5,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X5_R1.fastq.gz 18843X5_R2.fastq.gz,fastq fastq,11487744176.0,38038888.0,18843X5 R1.fastq.gz,0:151 1:151,A:3214900282;C:2532228300;G:2651065167;T:3089370892;N:179535,151,151,,,3214900282,2532228300,2651065167,3089370892,179535,SRX21375297,SRS18618389,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91483,0.91311,0.35213,0.35037,0.68347,0.68826,0.49832,0.49905,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25144,SRR25649165,SRX21375296,SRS18618388,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X6,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X6,18843X6,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X6_R1.fastq.gz 18843X6_R2.fastq.gz,fastq fastq,8690806510.0,28777505.0,18843X6 R1.fastq.gz,0:151 1:151,A:2346658651;C:2002583855;G:2108507319;T:2232918222;N:138463,151,151,,,2346658651,2002583855,2108507319,2232918222,138463,SRX21375296,SRS18618388,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91741,0.91785,0.21796,0.21778,0.6971,0.70102,0.49123,0.51016,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25145,SRR25649166,SRX21375295,SRS18618387,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X9,18689X9,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X9_R1.fastq.gz 18689X9_R2.fastq.gz,fastq fastq,9420964292.0,31195246.0,18689X9 R1.fastq.gz,0:151 1:151,A:2315675361;C:2390479538;G:2363596017;T:2351024167;N:189209,151,151,,,2315675361,2390479538,2363596017,2351024167,189209,SRX21375295,SRS18618387,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87883,0.87875,0.25078,0.24834,0.75394,0.75418,0.60036,0.59504,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25146,SRR25649167,SRX21375294,SRS18618386,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X2,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X2,18843X2,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X2_R2.fastq.gz 18843X2_R1.fastq.gz,fastq fastq,8319888298.0,27549299.0,18843X2 R1.fastq.gz,0:151 1:151,A:2316006657;C:1846379220;G:1965504688;T:2191867233;N:130500,151,151,,,2316006657,1846379220,1965504688,2191867233,130500,SRX21375294,SRS18618386,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90304,0.30055,0.3001,0.68345,0.6901,0.49306,0.48285,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25147,SRR25649168,SRX21375293,SRS18618385,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X3,18843X3,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X3_R1.fastq.gz 18843X3_R2.fastq.gz,fastq fastq,9351018676.0,30963638.0,18843X3 R1.fastq.gz,0:151 1:151,A:2555870224;C:2133006230;G:2246501165;T:2415491618;N:149439,151,151,,,2555870224,2133006230,2246501165,2415491618,149439,SRX21375293,SRS18618385,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91594,0.91512,0.21678,0.21621,0.72719,0.73117,0.52961,0.53327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25148,SRR25649169,SRX21375292,SRS18618384,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X1,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X1,18843X1,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X1_R1.fastq.gz 18843X1_R2.fastq.gz,fastq fastq,8760175608.0,29007204.0,18843X1 R1.fastq.gz,0:151 1:151,A:2335440655;C:2073187411;G:2210813716;T:2140593603;N:140223,151,151,,,2335440655,2073187411,2210813716,2140593603,140223,SRX21375292,SRS18618384,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.84641,0.8437,0.21898,0.21841,0.71301,0.72044,0.48661,0.49029,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25149,SRR25649170,SRX21375291,SRS18618383,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X9,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X9,19629X9,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X9_R1.fastq.gz 19629X9_R2.fastq.gz,fastq fastq,12342730940.0,40869970.0,19629X9 R1.fastq.gz,0:151 1:151,A:3339874828;C:2828928610;G:2945452577;T:3228218292;N:256633,151,151,,,3339874828,2828928610,2945452577,3228218292,256633,SRX21375291,SRS18618383,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90738,0.8127,0.19825,0.17409,0.73385,0.74659,0.54306,0.55304,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25150,SRR25649171,SRX21375290,SRS18618382,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X1,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X1,18689X1,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X1_R1.fastq.gz 18689X1_R2.fastq.gz,fastq fastq,7723999112.0,25576156.0,18689X1 R1.fastq.gz,0:151 1:151,A:1938376895;C:1923902263;G:1896332244;T:1965229370;N:158340,151,151,,,1938376895,1923902263,1896332244,1965229370,158340,SRX21375290,SRS18618382,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87233,0.87262,0.28456,0.28071,0.73858,0.7414,0.60785,0.61428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25151,SRR25649172,SRX21375289,SRS18618381,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X5,18689X5,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X5_R1.fastq.gz 18689X5_R2.fastq.gz,fastq fastq,8136028886.0,26940493.0,18689X5 R1.fastq.gz,0:151 1:151,A:2015403368;C:2051480513;G:2023331135;T:2045661742;N:152128,151,151,,,2015403368,2051480513,2023331135,2045661742,152128,SRX21375289,SRS18618381,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88067,0.88216,0.24575,0.2425,0.75018,0.75073,0.59361,0.61451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25152,SRR25649173,SRX21375288,SRS18618380,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X11,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X11,18689X11,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X11_R1.fastq.gz 18689X11_R2.fastq.gz,fastq fastq,9515677834.0,31508867.0,18689X11 R1.fastq.gz,0:151 1:151,A:2274021342;C:2477750132;G:2454285243;T:2309429465;N:191652,151,151,,,2274021342,2477750132,2454285243,2309429465,191652,SRX21375288,SRS18618380,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87714,0.87737,0.2476,0.24538,0.77968,0.78248,0.63108,0.65333,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25153,SRR25649174,SRX21375287,SRS18618379,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X8,18843X8,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X8_R1.fastq.gz 18843X8_R2.fastq.gz,fastq fastq,7615135964.0,25215682.0,18843X8 R1.fastq.gz,0:151 1:151,A:2157897532;C:1663478819;G:1764954395;T:2028683751;N:121467,151,151,,,2157897532,1663478819,1764954395,2028683751,121467,SRX21375287,SRS18618379,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91455,0.91333,0.34885,0.34782,0.69467,0.70167,0.50339,0.51371,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25154,SRR25649175,SRX21375286,SRS18618378,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X9,18843X9,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X9_R1.fastq.gz 18843X9_R2.fastq.gz,fastq fastq,8819654206.0,29204153.0,18843X9 R1.fastq.gz,0:151 1:151,A:2383706177;C:2044504407;G:2140881818;T:2250422256;N:139548,151,151,,,2383706177,2044504407,2140881818,2250422256,139548,SRX21375286,SRS18618378,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90437,0.21274,0.21235,0.72604,0.73164,0.52888,0.52909,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25155,SRR25649176,SRX21375285,SRS18618377,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X7,18843X7,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X7_R1.fastq.gz 18843X7_R2.fastq.gz,fastq fastq,9614914732.0,31837466.0,18843X7 R1.fastq.gz,0:151 1:151,A:2577032258;C:2236946505;G:2389573431;T:2411211222;N:151316,151,151,,,2577032258,2236946505,2389573431,2411211222,151316,SRX21375285,SRS18618377,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.8913,0.88909,0.31019,0.30978,0.71721,0.72557,0.50815,0.52261,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25156,SRR25649177,SRX21375284,SRS18618376,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X3,18689X3,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X3_R1.fastq.gz 18689X3_R2.fastq.gz,fastq fastq,8819353112.0,29203156.0,18689X3 R1.fastq.gz,0:151 1:151,A:2342877591;C:2071139579;G:2035896879;T:2369259787;N:179276,151,151,,,2342877591,2071139579,2035896879,2369259787,179276,SRX21375284,SRS18618376,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.85514,0.85429,0.35095,0.34608,0.72985,0.73077,0.51131,0.53375,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25157,SRR25649178,SRX21375283,SRS18618375,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X7,18689X7,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X7_R1.fastq.gz 18689X7_R2.fastq.gz,fastq fastq,8986035368.0,29755084.0,18689X7 R1.fastq.gz,0:151 1:151,A:2169723143;C:2326462981;G:2292317481;T:2197350043;N:181720,151,151,,,2169723143,2326462981,2292317481,2197350043,181720,SRX21375283,SRS18618375,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89254,0.89285,0.22562,0.22356,0.74911,0.75089,0.6409,0.65585,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25158,SRR25649179,SRX21375282,SRS18618374,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X12,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:spleen|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X12,18689X12,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X12_R1.fastq.gz 18689X12_R2.fastq.gz,fastq fastq,9338495642.0,30922171.0,18689X12 R1.fastq.gz,0:151 1:151,A:2151902218;C:2516218122;G:2484485366;T:2185704377;N:185559,151,151,,,2151902218,2516218122,2484485366,2185704377,185559,SRX21375282,SRS18618374,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88601,0.8889,0.17526,0.17449,0.81702,0.81801,0.46118,0.46609,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25159,SRR25649180,SRX21375281,SRS18618373,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X4,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:kidney|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X4,18689X4,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X4_R1.fastq.gz 18689X4_R2.fastq.gz,fastq fastq,9931670150.0,32886325.0,18689X4 R1.fastq.gz,0:151 1:151,A:2494588549;C:2471174839;G:2445771402;T:2519940959;N:194401,151,151,,,2494588549,2471174839,2445771402,2519940959,194401,SRX21375281,SRS18618373,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87391,0.87402,0.31383,0.30879,0.73789,0.74014,0.63365,0.63903,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25160,SRR25649181,SRX21375280,SRS18618372,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X8,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X8,19629X8,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X8_R2.fastq.gz 19629X8_R1.fastq.gz,fastq fastq,10758135430.0,35622965.0,19629X8 R1.fastq.gz,0:151 1:151,A:2991372806;C:2398155523;G:2517276916;T:2851104238;N:225947,151,151,,,2991372806,2398155523,2517276916,2851104238,225947,SRX21375280,SRS18618372,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88839,0.89055,0.23357,0.23344,0.72592,0.72851,0.53343,0.53081,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25161,SRR25649182,SRX21375279,SRS18618371,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X7,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X7,19629X7,Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X7_R1.fastq.gz 19629X7_R2.fastq.gz,fastq fastq,11738178884.0,38868142.0,19629X7 R1.fastq.gz,0:151 1:151,A:3192358555;C:2674045852;G:2784070515;T:3087458659;N:245303,151,151,,,3192358555,2674045852,2784070515,3087458659,245303,SRX21375279,SRS18618371,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.9074,0.90829,0.20853,0.20916,0.74115,0.74369,0.53704,0.55385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
34262,SRR31595085,SRX26959911,SRS23429841,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Alarm substances treatment Group,,CAS,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CAS group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CAS group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances,CAS OE,CAS OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz,fastq fastq,54518124857.0,458135503.0,CAS S1 L001 R1 001.fastq.gz,0:28 1:91,A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809,28,91,,,15384916510,12274547586,14008767028,12837270924,12622809,SRX26959911,SRS23429841,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
34263,SRR31595086,SRX26959910,SRS23429840,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Blank control group,,CTR,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CTR group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CTR group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB strain zebrafish olfactory epithelium,CTR OE,CTR OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz,fastq fastq,50773421790.0,426667410.0,CTR S1 L001 R1 001.fastq.gz,0:28 1:91,A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821,28,91,,,14105926130,11510784907,13135577448,12011516484,9616821,SRX26959910,SRS23429840,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
36236,SRR33613689,SRX28842041,SRS25072235,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,ea 6,,strain:Not collected|isolate:aa 4|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:Danio rerio zebrafishcellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,ea 6,ea 6,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100087-e13_a4.R1.raw.fastq.gz L1HJB2100087-e13_a4.R2.raw.fastq.gz,fastq fastq,4387314664.0,14527532.0,L1HJB2100087 e13 a4.R1.raw.fastq.gz,0:151 1:151,A:1181219785;C:999854316;G:1021151141;T:1185029538;N:59884,151,151,,,1181219785,999854316,1021151141,1185029538,59884,SRX28842041,SRS25072235,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
36237,SRR33613690,SRX28842040,SRS25072236,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,ea 5,,strain:Not collected|isolate:aa 3|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:Danio rerio zebrafishcellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,ea 5,ea 5,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100086-e13_a3.R1.raw.fastq.gz L1HJB2100086-e13_a3.R2.raw.fastq.gz,fastq fastq,4718170160.0,15623080.0,L1HJB2100086 e13 a3.R1.raw.fastq.gz,0:151 1:151,A:1297970572;C:1052292935;G:1069086913;T:1298756019;N:63721,151,151,,,1297970572,1052292935,1069086913,1298756019,63721,SRX28842040,SRS25072236,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
36238,SRR33613691,SRX28842039,SRS25072234,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,ea 4,,strain:Not collected|isolate:aa 2|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:Danio rerio zebrafishcellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,ea 4,ea 4,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100085-e13_a2.R1.raw.fastq.gz L1HJB2100085-e13_a2.R2.raw.fastq.gz,fastq fastq,4102870528.0,13585664.0,L1HJB2100085 e13 a2.R1.raw.fastq.gz,0:151 1:151,A:1108518064;C:932530532;G:950570756;T:1111194555;N:56621,151,151,,,1108518064,932530532,950570756,1111194555,56621,SRX28842039,SRS25072234,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
36239,SRR33613692,SRX28842038,SRS25072233,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,eA 3,,strain:Not collected|isolate:AA 4|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:Danio rerio zebrafishcellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,eA 3,eA 3,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100083-e13_AA4.R1.raw.fastq.gz L1HJB2100083-e13_AA4.R2.raw.fastq.gz,fastq fastq,4149242628.0,13739214.0,L1HJB2100083 e13 AA4.R1.raw.fastq.gz,0:151 1:151,A:1147822173;C:922103806;G:936893354;T:1142368362;N:54933,151,151,,,1147822173,922103806,936893354,1142368362,54933,SRX28842038,SRS25072233,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
36240,SRR33613693,SRX28842037,SRS25072232,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,eA 2,,strain:Not collected|isolate:AA 3|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:Danio rerio zebrafishcellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,eA 2,eA 2,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100082-e13_AA3.R1.raw.fastq.gz L1HJB2100082-e13_AA3.R2.raw.fastq.gz,fastq fastq,4322107126.0,14311613.0,L1HJB2100082 e13 AA3.R1.raw.fastq.gz,0:151 1:151,A:1174477372;C:977793303;G:994707829;T:1175046923;N:81699,151,151,,,1174477372,977793303,994707829,1175046923,81699,SRX28842037,SRS25072232,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
36241,SRR33613694,SRX28842036,SRS25072231,SRP586122,PRJNA1264536,Transcriptomic analysis of zebrafish liver reveals effects of ehd3 knockout on fatty acid metabolism,PRJNA1264536,Other,This study aims to investigate the impact of ehd3 gene knockout on liver transcriptome profiles and fatty acid metabolism in zebrafish Danio rerio. By comparing the transcriptomic differences between ehd3 Homozygous mutants and wild type controls we sought to identify differentially expressed genes and pathways involved in lipid synthesis elongation and desaturation. The findings will enhance our understanding of the regulatory role of EHD3 in hepatic fatty acid homeostasis and provide insights into the genetic mechanisms underlying lipid metabolism. This research is relevant to both fundamental studies in metabolic biology and potential applications in improving fish nutritional quality and understanding lipid related disorders.,,,,,eA 1,,strain:Not collected|isolate:AA 2|breed:Artemia|cultivar:Not collected|ecotype:Not collected|age:4 mpf|dev stage:Adult fish|collection date:2025 01 03|geo loc name:China:Xiamen|sex:male|tissue:liver|danio rerio zebrafish:cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Danionidae; Danioninae; Danio|BioSampleModel:Model organism or animal,,,,,,,,,liver RNA seq,eA 1,eA 1,Transcriptome data from two groups of gene knockouts in zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP586122,,,L1HJB2100081-e13_AA2.R1.raw.fastq.gz L1HJB2100081-e13_AA2.R2.raw.fastq.gz,fastq fastq,4345265392.0,14388296.0,L1HJB2100081 e13 AA2.R1.raw.fastq.gz,0:151 1:151,A:1198935259;C:966182053;G:982645751;T:1197420171;N:82158,151,151,,,1198935259,966182053,982645751,1197420171,82158,SRX28842036,SRS25072231,SRA2131923,Jimei University|Fisheries College,Jimei University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-05-18,Adult,Adult,Liver,Liver and Biliary System
37103,SRR891512,SRX298192,SRS673882,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio blood,,sex:missing|strain:wild type|tissue:blood|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio blood,zebrafish blood,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1020Application ReadForward11Application ReadReverse52,SRP024369,,,lane6_NoIndex_L006_R2_cat.fastq lane6_NoIndex_L006_R1_cat.fastq,fastq fastq,2122070832.0,20804616.0,Transcriptome of zebrafish Danio rerio blood,0:51 1:51,A:508869849;C:550502747;G:580539251;T:481927903;N:231082,51,51,,,508869849,550502747,580539251,481927903,231082,SRX298192,SRS673882,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.78255,0.77496,0.03257,0.03239,0.75672,0.75542,0.44135,0.44382,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-06-10,Adult,Adult,Blood,Hematopoietic System
37104,SRR891511,SRX298191,SRS673881,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio brain,,sex:missing|strain:wild type|tissue:brain|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio brain,zebrafish brain,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1020Application ReadForward11Application ReadReverse52,SRP024369,,,lane5_NoIndex_L005_R2_cat.fastq lane5_NoIndex_L005_R1_cat.fastq,fastq fastq,1597586730.0,15662615.0,Transcriptome of zebrafish Danio rerio brain,0:51 1:51,A:408194270;C:393362321;G:391996499;T:403728707;N:304933,51,51,,,408194270,393362321,391996499,403728707,304933,SRX298191,SRS673881,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.8957,0.89547,0.13204,0.13077,0.70514,0.70504,0.48733,0.48703,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-10-10,Adult,Adult,Brain,Nervous System
37105,SRR891510,SRX298190,SRS673880,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio muscle,,sex:missing|strain:wild type|tissue:muscle|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio muscle,zebrafish muscle,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1020Application ReadForward11Application ReadReverse52,SRP024369,,,lane4_NoIndex_L004_R1_cat.fastq lane4_NoIndex_L004_R2_cat.fastq,fastq fastq,1895673468.0,18585034.0,Transcriptome of zebrafish Danio rerio muscle,0:51 1:51,A:461627994;C:495899684;G:489490468;T:448396921;N:258401,51,51,,,461627994,495899684,489490468,448396921,258401,SRX298190,SRS673880,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.90619,0.93507,0.0338,0.03473,0.79267,0.78683,0.45256,0.45438,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-10-10,Adult,Adult,Muscle,Muscular System
37106,SRR891504,SRX298189,SRS673879,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio liver,,sex:missing|strain:wild type|tissue:liver|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio liver,Zebrafish Liver,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1020Application ReadForward11Application ReadReverse52,SRP024369,,,lane2_NoIndex_L002_R1_cat.fastq lane2_NoIndex_L002_R2_cat.fastq,fastq fastq,2901183144.0,28442972.0,Transcriptome of zebrafish Danio rerio Liver,0:51 1:51,A:728201287;C:715925650;G:737506674;T:719033716;N:515817,51,51,,,728201287,715925650,737506674,719033716,515817,SRX298189,SRS673879,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.87667,0.87728,0.03607,0.03788,0.89351,0.89471,0.16094,0.15975,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-10-10,Adult,Adult,Liver,Liver and Biliary System