rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9367,ERR145653,ERX121572,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 B seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_B_1.fq.gz WW3_B_2.fq.gz,fastq fastq,4347695086.0,21523243.0,E MTAB 1155:WW3 B,0:101 1:101,A:1074237454;C:1092333862;G:1102729864;T:1065390007;N:13003899,101,101,,,1074237454,1092333862,1102729864,1065390007,13003899,ERX121572,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95796,0.9583,0.02413,0.02313,0.83946,0.8338,0.51717,0.51633,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9368,ERR145654,ERX121560,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 A seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_A_1.fq.gz WW4_A_2.fq.gz,fastq fastq,80948470.0,400735.0,E MTAB 1155:WW4 A,0:101 1:101,A:21174054;C:19268727;G:19622428;T:20880804;N:2457,101,101,,,21174054,19268727,19622428,20880804,2457,ERX121560,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93674,0.92652,0.0383,0.03971,0.84776,0.86028,0.52028,0.51601,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9369,ERR145639,ERX121583,ERS151247,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW4 F M pooled fish,SAMEA1487357,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487357|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW4 seq,CW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW4_1.fq.gz CW4_2.fq.gz,fastq fastq,7322391324.0,36249462.0,E MTAB 1155:CW4,0:101 1:101,A:1915177797;C:1750141576;G:1768328049;T:1887892000;N:851902,101,101,,,1915177797,1750141576,1768328049,1887892000,851902,ERX121583,ERS151247,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94177,0.93855,0.04669,0.04835,0.81227,0.81663,0.5297,0.53381,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9370,ERR145632,ERX121582,ERS151246,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH2 F M pooled fish,SAMEA1487358,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487358|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH2 seq,CH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH2_1.fq.gz CH2_2.fq.gz,fastq fastq,6008384960.0,29744480.0,E MTAB 1155:CH2,0:101 1:101,A:1551084475;C:1456651824;G:1467972620;T:1531930144;N:745897,101,101,,,1551084475,1456651824,1467972620,1531930144,745897,ERX121582,ERS151246,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94484,0.94325,0.04187,0.04238,0.81448,0.8172,0.46639,0.50253,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9371,ERR145634,ERX121581,ERS151245,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH4 F M pooled fish,SAMEA1487361,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487361|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH4 seq,CH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH4_1.fq.gz CH4_2.fq.gz,fastq fastq,5647385104.0,27957352.0,E MTAB 1155:CH4,0:101 1:101,A:1469982057;C:1356659164;G:1371916498;T:1448143269;N:684116,101,101,,,1469982057,1356659164,1371916498,1448143269,684116,ERX121581,ERS151245,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93865,0.93633,0.0439,0.04446,0.80549,0.80864,0.53045,0.51098,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9372,ERR145651,ERX121579,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 B seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_B_1.fq.gz WW2_B_2.fq.gz,fastq fastq,4738967672.0,23460236.0,E MTAB 1155:WW2 B,0:101 1:101,A:1175576318;C:1183749238;G:1198839519;T:1166587116;N:14215481,101,101,,,1175576318,1183749238,1198839519,1166587116,14215481,ERX121579,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95497,0.95617,0.02438,0.0233,0.82909,0.82455,0.51164,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9373,ERR145652,ERX121578,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 A seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_A_1.fq.gz WW3_A_2.fq.gz,fastq fastq,229808532.0,1137666.0,E MTAB 1155:WW3 A,0:101 1:101,A:59360822;C:55502890;G:56337453;T:58600433;N:6934,101,101,,,59360822,55502890,56337453,58600433,6934,ERX121578,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93623,0.92715,0.03151,0.03268,0.83735,0.84952,0.52265,0.5038,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9374,ERR145649,ERX121577,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 B seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_B_1.fq.gz WW1_B_2.fq.gz,fastq fastq,7635373356.0,37798878.0,E MTAB 1155:WW1 B,0:101 1:101,A:1902965653;C:1900547622;G:1920575326;T:1888470954;N:22813801,101,101,,,1902965653,1900547622,1920575326,1888470954,22813801,ERX121577,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95977,0.95988,0.02636,0.02563,0.84279,0.83808,0.52131,0.45646,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9375,ERR145636,ERX121576,ERS151244,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW2 F M pooled fish,SAMEA1487364,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487364|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW2 seq,CW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW2_1.fq.gz CW2_2.fq.gz,fastq fastq,7748012798.0,38356499.0,E MTAB 1155:CW2,0:101 1:101,A:2015650126;C:1864022271;G:1874527501;T:1992894699;N:918201,101,101,,,2015650126,1864022271,1874527501,1992894699,918201,ERX121576,ERS151244,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94537,0.94243,0.04249,0.04301,0.82213,0.82552,0.52811,0.53747,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9376,ERR145646,ERX121571,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 A seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_A_1.fq.gz WH4_A_2.fq.gz,fastq fastq,812883148.0,4024174.0,E MTAB 1155:WH4 A,0:101 1:101,A:209997189;C:196285019;G:198925947;T:207278009;N:396984,101,101,,,209997189,196285019,198925947,207278009,396984,ERX121571,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94663,0.91942,0.03602,0.03591,0.8424,0.85462,0.51702,0.51147,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9377,ERR145647,ERX121570,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 B seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_B_1.fq.gz WH4_B_2.fq.gz,fastq fastq,10768144694.0,53307647.0,E MTAB 1155:WH4 B,0:101 1:101,A:2682817583;C:2706807352;G:2714533015;T:2652309644;N:11677100,101,101,,,2682817583,2706807352,2714533015,2652309644,11677100,ERX121570,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95867,0.96056,0.02378,0.02413,0.83609,0.83889,0.43331,0.44066,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9378,ERR145655,ERX121569,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 B seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_B_1.fq.gz WW4_B_2.fq.gz,fastq fastq,6455936968.0,31960084.0,E MTAB 1155:WW4 B,0:101 1:101,A:1610738878;C:1605252294;G:1623372987;T:1597311219;N:19261590,101,101,,,1610738878,1605252294,1623372987,1597311219,19261590,ERX121569,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.96085,0.96101,0.02863,0.02731,0.84995,0.8452,0.52157,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9379,ERR145633,ERX121568,ERS151240,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH3 F M pooled fish,SAMEA1487363,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487363|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH3 seq,CH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH3_1.fq.gz CH3_2.fq.gz,fastq fastq,6146419640.0,30427820.0,E MTAB 1155:CH3,0:101 1:101,A:1596666196;C:1479913350;G:1493612614;T:1575480940;N:746540,101,101,,,1596666196,1479913350,1493612614,1575480940,746540,ERX121568,ERS151240,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93901,0.93723,0.04362,0.04417,0.79715,0.7977,0.51473,0.52412,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9380,ERR145650,ERX121567,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 A seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_A_1.fq.gz WW2_A_2.fq.gz,fastq fastq,280038054.0,1386327.0,E MTAB 1155:WW2 A,0:101 1:101,A:72831492;C:67021049;G:68232991;T:71942949;N:9573,101,101,,,72831492,67021049,68232991,71942949,9573,ERX121567,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93032,0.9187,0.03207,0.03356,0.82852,0.84139,0.52376,0.52436,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9381,ERR145637,ERX121565,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 A seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_A_1.fq.gz CW3_A_2.fq.gz,fastq fastq,2104292580.0,10417290.0,E MTAB 1155:CW3 A,0:101 1:101,A:547829220;C:504948167;G:510803037;T:540521191;N:190965,101,101,,,547829220,504948167,510803037,540521191,190965,ERX121565,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93423,0.92981,0.04776,0.04835,0.81245,0.81471,0.51349,0.4822,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9382,ERR145631,ERX121564,ERS151237,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH1 F M pooled fish,SAMEA1487356,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487356|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH1 seq,CH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH1_1.fq.gz CH1_2.fq.gz,fastq fastq,7734471526.0,38289463.0,E MTAB 1155:CH1,0:101 1:101,A:1980474194;C:1892305985;G:1907192207;T:1953595996;N:903144,101,101,,,1980474194,1892305985,1907192207,1953595996,903144,ERX121564,ERS151237,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94403,0.94213,0.03862,0.03913,0.82309,0.82556,0.49626,0.49773,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9383,ERR145635,ERX121562,ERS151235,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW1 F M pooled fish,SAMEA1487366,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487366|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW1 seq,CW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW1_1.fq.gz CW1_2.fq.gz,fastq fastq,6202716838.0,30706519.0,E MTAB 1155:CW1,0:101 1:101,A:1612950873;C:1492406749;G:1504306823;T:1592361004;N:691389,101,101,,,1612950873,1492406749,1504306823,1592361004,691389,ERX121562,ERS151235,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94448,0.94226,0.04304,0.04379,0.81296,0.81489,0.5237,0.52588,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9384,ERR145648,ERX121561,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 A seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_A_1.fq.gz WW1_A_2.fq.gz,fastq fastq,330954174.0,1638387.0,E MTAB 1155:WW1 A,0:101 1:101,A:86485807;C:78916128;G:80103844;T:85437370;N:11025,101,101,,,86485807,78916128,80103844,85437370,11025,ERX121561,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93321,0.92294,0.03445,0.03581,0.84133,0.85267,0.54253,0.53593,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9385,ERR145638,ERX121559,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 B seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_B_1.fq.gz CW3_B_2.fq.gz,fastq fastq,6504819756.0,32202078.0,E MTAB 1155:CW3 B,0:101 1:101,A:1653674963;C:1600212014;G:1606437826;T:1637400265;N:7094688,101,101,,,1653674963,1600212014,1606437826,1637400265,7094688,ERX121559,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94253,0.94443,0.03782,0.03856,0.80661,0.80801,0.49414,0.51667,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9386,ERR147028,ERX122956,ERS151238,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH3 F M pooled fish,SAMEA1487362,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH3 seq,WH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH3_1.fq.gz WH3_2.fq.gz,fastq fastq,3197103894.0,15827247.0,E MTAB 1155:WH3,0:101 1:101,A:829020337;C:767623553;G:780642278;T:818288216;N:1529510,101,101,,,829020337,767623553,780642278,818288216,1529510,ERX122956,ERS151238,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94791,0.91975,0.03726,0.03735,0.84291,0.85622,0.4972,0.50314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9387,ERR147027,ERX122955,ERS151236,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH2 F M pooled fish,SAMEA1487365,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487365|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH2 seq,WH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH2_1.fq.gz WH2_2.fq.gz,fastq fastq,3455989922.0,17108861.0,E MTAB 1155:WH2,0:101 1:101,A:902145358;C:824320050;G:837200815;T:890816825;N:1506874,101,101,,,902145358,824320050,837200815,890816825,1506874,ERX122955,ERS151236,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94863,0.92001,0.04084,0.04066,0.83796,0.85263,0.5275,0.51735,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9388,ERR147026,ERX122954,ERS151243,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH1 F M pooled fish,SAMEA1487369,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487369|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH1 seq,WH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH1_1.fq.gz WH1_2.fq.gz,fastq fastq,3005524064.0,14878832.0,E MTAB 1155:WH1,0:101 1:101,A:780146739;C:722416478;G:730307409;T:771476282;N:1177156,101,101,,,780146739,722416478,730307409,771476282,1177156,ERX122954,ERS151243,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94764,0.92072,0.03746,0.03773,0.83416,0.84831,0.42239,0.51505,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9711,ERR3366000,ERX3390288,ERS3506636,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 3,SAMEA5702979,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 3 p,WT 5dpf whole 3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz,fastq fastq,7638506536.0,25293068.0,E MTAB 8029:WT 5dpf whole 3 ,0:151 1:151,A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553,151,151,,,2033085216,1787203019,1834311569,1982924179,982553,ERX3390288,ERS3506636,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92943,0.93349,0.06443,0.06476,0.67008,0.68489,0.45244,0.47512,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9712,ERR3365999,ERX3390287,ERS3506635,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 2,SAMEA5702978,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 2 p,WT 5dpf whole 2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz,fastq fastq,8029356446.0,26587273.0,E MTAB 8029:WT 5dpf whole 2 ,0:151 1:151,A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810,151,151,,,2111720421,1902949602,1956400199,2057162414,1123810,ERX3390287,ERS3506635,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93664,0.9394,0.06211,0.06234,0.67036,0.68416,0.44709,0.4713,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9713,ERR3365998,ERX3390286,ERS3506634,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 1,SAMEA5702977,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 1 p,WT 5dpf whole 1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz,fastq fastq,7581314682.0,25103691.0,E MTAB 8029:WT 5dpf whole 1 ,0:151 1:151,A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540,151,151,,,2028089715,1768357820,1809746152,1974047455,1073540,ERX3390286,ERS3506634,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92712,0.93122,0.06876,0.06853,0.66464,0.67537,0.46592,0.47176,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9714,ERR3365997,ERX3390285,ERS3506633,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl2,SAMEA5702976,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl2 p,c386C T het 5dpf whl2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz,fastq fastq,7431512716.0,24607658.0,E MTAB 8029:c386C T het 5dpf whl 2 ,0:151 1:151,A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572,151,151,,,1981584337,1740735155,1776201259,1931922393,1069572,ERX3390285,ERS3506633,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92957,0.933,0.0653,0.06445,0.66967,0.6788,0.46228,0.46392,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9715,ERR3365996,ERX3390284,ERS3506632,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl1,SAMEA5702975,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl1 p,c386C T het 5dpf whl1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz,fastq fastq,7350140024.0,24338212.0,E MTAB 8029:c386C T het 5dpf whl 1 ,0:151 1:151,A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274,151,151,,,1930881649,1748604586,1790297791,1879354724,1001274,ERX3390284,ERS3506632,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93663,0.9384,0.05835,0.05828,0.66557,0.67588,0.467,0.46407,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9716,ERR3365995,ERX3390283,ERS3506631,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c.386C T het 5dpf whl3,SAMEA5702974,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c.386C T het 5dpf whl3 p,c.386C T het 5dpf whl3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz,fastq fastq,6059681642.0,20065171.0,E MTAB 8029:c386C T het 5dpf whl 3 ,0:151 1:151,A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092,151,151,,,1604034432,1423963595,1467519505,1563303018,861092,ERX3390283,ERS3506631,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93301,0.9374,0.0658,0.06581,0.66681,0.68503,0.46139,0.47743,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10060,ERR4795364,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz,fastq,5410723202.0,71707309.0,E MTAB 9727:Sample 4,0:75.46 1:0,A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666,75,0,,,1330416803,531269504,734031980,2814959249,45666,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.33614,,0.21532,,0.99019,,0.41002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10061,ERR4795365,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz,fastq,5414184547.0,71707309.0,E MTAB 9727:Sample 4 1,0:0 1:75.50,A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967,0,75,,,1582938104,1052565419,1177180395,1600161662,1338967,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.84976,,0.28521,,0.85038,,0.5124,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10062,ERR4795362,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz,fastq,4823193891.0,63965519.0,E MTAB 9727:Sample 3,0:75.40 1:0,A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086,75,0,,,1323978162,446831209,581746343,2470114091,524086,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.36549,,0.19722,,0.95552,,0.4702,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10063,ERR4795363,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz,fastq,4828889391.0,63965519.0,E MTAB 9727:Sample 3 1,0:0 1:75.49,A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756,0,75,,,1434099697,964508763,893584575,1534727600,1968756,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.85811,,0.26231,,0.82731,,0.48618,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10064,ERR4795360,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz,fastq,5598371393.0,74235388.0,E MTAB 9727:Sample 2,0:75.41 1:0,A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655,75,0,,,1526486973,558020193,717587491,2795646081,630655,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.28059,,0.19252,,0.96404,,0.4874,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10065,ERR4795361,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz,fastq,5600151371.0,74235388.0,E MTAB 9727:Sample 2 1,0:0 1:75.44,A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060,0,75,,,1850568176,1035622971,1071138281,1640475883,2346060,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.7679,,0.30371,,0.82651,,0.43401,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10066,ERR4795358,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz,fastq,4996502316.0,66258508.0,E MTAB 9727:Sample 1,0:75.41 1:0,A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936,75,0,,,1330744174,451622042,591151500,2622422664,561936,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.29754,,0.17671,,0.9669,,0.45463,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10067,ERR4795359,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz,fastq,4999908389.0,66258508.0,E MTAB 9727:Sample 1 1,0:0 1:75.46,A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512,0,75,,,1591945117,933968124,986108614,1485824022,2062512,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.81333,,0.2466,,0.83027,,0.51572,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10374,ERR8058375,ERX7625096,ERS10119356,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 3,SAMEA12512752,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 3 p,Morphine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz,fastq fastq,11175776640.0,44348320.0,E MTAB 11346:NG 10331 4M lib138515 4790 6 ,0:126 1:126,A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329,126,126,,,3058552548,2537121022,2531362154,3047376587,1364329,ERX7625096,ERS10119356,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93345,0.93836,0.09826,0.09482,0.69497,0.69968,0.46885,0.46966,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10375,ERR8058374,ERX7625095,ERS10119355,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 2,SAMEA12512751,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 2 p,Morphine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz,fastq fastq,10428424776.0,41382638.0,E MTAB 11346:NG 10331 3M lib138512 4790 5 ,0:126 1:126,A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201,126,126,,,2840226558,2379827926,2389813154,2817428937,1128201,ERX7625095,ERS10119355,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94204,0.9476,0.09827,0.09565,0.7008,0.70483,0.47435,0.47651,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10376,ERR8058373,ERX7625094,ERS10119354,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 1,SAMEA12512750,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 1 p,Morphine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz,fastq fastq,13158093312.0,52214656.0,E MTAB 11346:NG 10331 2M lib138509 4790 5 ,0:126 1:126,A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572,126,126,,,3613282182,2969954628,2964948806,3608471124,1436572,ERX7625094,ERS10119354,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93755,0.93735,0.11204,0.10849,0.67838,0.68335,0.45142,0.46509,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10377,ERR8058372,ERX7625093,ERS10119353,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 3,SAMEA12512749,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 3 p,Control 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz,fastq fastq,14106514968.0,55978234.0,E MTAB 11346:NG 10331 4C lib138514 4790 6 ,0:126 1:126,A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393,126,126,,,3862641975,3195634147,3187866318,3858673135,1699393,ERX7625093,ERS10119353,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93657,0.93813,0.09783,0.09438,0.68925,0.69605,0.4741,0.47037,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10378,ERR8058371,ERX7625092,ERS10119352,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 2,SAMEA12512748,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 2 p,Control 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz,fastq fastq,8889952680.0,35277590.0,E MTAB 11346:NG 10331 3C lib138511 4790 5 ,0:126 1:126,A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902,126,126,,,2424658667,2024699093,2023098669,2416527349,968902,ERX7625092,ERS10119352,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94168,0.94149,0.09632,0.09404,0.68996,0.69672,0.46007,0.47123,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10379,ERR8058370,ERX7625091,ERS10119351,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 1,SAMEA12512747,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 1 p,Control 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz,fastq fastq,12714421356.0,50454053.0,E MTAB 11346:NG 10331 2C lib138508 4790 5 ,0:126 1:126,A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272,126,126,,,3470625985,2894721473,2886656166,3461036460,1381272,ERX7625091,ERS10119351,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93951,0.93975,0.10489,0.10173,0.68134,0.68702,0.45337,0.44545,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10380,ERR8058369,ERX7625090,ERS10119350,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 3,SAMEA12512746,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 3 p,Cocaine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz,fastq fastq,9574359984.0,37993492.0,E MTAB 11346:NG 10331 4CC lib138516 4790 6 ,0:126 1:126,A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518,126,126,,,2623103101,2170327733,2166494677,2613276955,1157518,ERX7625090,ERS10119350,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.9366,0.93856,0.10196,0.09901,0.69018,0.69611,0.46501,0.46917,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10381,ERR8058368,ERX7625089,ERS10119349,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 2,SAMEA12512745,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 2 p,Cocaine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz,fastq fastq,6977861604.0,27689927.0,E MTAB 11346:NG 10331 3CC lib138513 4828 1 ,0:126 1:126,A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359,126,126,,,1938593544,1560242508,1564690065,1913028128,1307359,ERX7625089,ERS10119349,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94226,0.9472,0.10354,0.10202,0.69911,0.69891,0.4749,0.47595,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10382,ERR8058367,ERX7625088,ERS10119348,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 1,SAMEA12512744,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 1 p,Cocaine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz,fastq fastq,13608728532.0,54002891.0,E MTAB 11346:NG 10331 2CC lib138510 4790 5 ,0:126 1:126,A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601,126,126,,,3713185950,3097562409,3088976816,3707538756,1464601,ERX7625088,ERS10119348,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93921,0.94011,0.104,0.10075,0.68043,0.68523,0.44482,0.4591,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
11238,ERR10782555,ERX10233132,ERS14439197,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 6,E MTAB 12503:Sample 6,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 6 p,Sample 6 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz,fastq fastq,14809693138.0,49038719.0,E MTAB 12503:20170530.A 6 R,0:151 1:151,A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269,151,151,,,4069749497,3367864217,3430269434,3928390721,13419269,ERX10233132,ERS14439197,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.83945,0.69977,0.27269,0.22488,0.74523,0.77654,0.4899,0.4358,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11239,ERR10782554,ERX10233131,ERS14439196,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 5,E MTAB 12503:Sample 5,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 5 p,Sample 5 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz,fastq fastq,14954968728.0,49519764.0,E MTAB 12503:20170530.A 5 R,0:151 1:151,A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280,151,151,,,4063340262,3440933120,3455723079,3981396987,13575280,ERX10233131,ERS14439196,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.85891,0.86859,0.28842,0.28866,0.7349,0.75051,0.45532,0.49145,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11240,ERR10782553,ERX10233130,ERS14439195,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 2,E MTAB 12503:Sample 2,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 2 p,Sample 2 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz,fastq fastq,16267571562.0,53866131.0,E MTAB 12503:20170530.A 2 R,0:151 1:151,A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668,151,151,,,4395815325,3765428574,3780844712,4310729283,14753668,ERX10233130,ERS14439195,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.86977,0.8727,0.28497,0.28427,0.70763,0.72301,0.47478,0.47986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11241,ERR10782552,ERX10233129,ERS14439194,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 1,E MTAB 12503:Sample 1,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 1 p,Sample 1 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz,fastq fastq,15446599662.0,51147681.0,E MTAB 12503:20170530.A 1 R,0:151 1:151,A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332,151,151,,,4289931639,3451135010,3474244788,4217248893,14039332,ERX10233129,ERS14439194,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.90114,0.90507,0.32128,0.32127,0.70232,0.71956,0.47336,0.47528,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11242,ERR10782551,ERX10233128,ERS14439193,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 7,E MTAB 12503:Sample 7,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 7 p,Sample 7 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz,fastq fastq,12726557236.0,42140918.0,E MTAB 12503:20170530.A 7 R,0:151 1:151,A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382,151,151,,,3510176970,2879679978,2932244172,3392911734,11544382,ERX10233128,ERS14439193,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88531,0.88678,0.33279,0.3329,0.73545,0.74992,0.52548,0.52864,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11243,ERR10782550,ERX10233127,ERS14439192,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 4,E MTAB 12503:Sample 4,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 4 p,Sample 4 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz,fastq fastq,15697575554.0,51978727.0,E MTAB 12503:20170530.A 4 R,0:151 1:151,A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133,151,151,,,4256444510,3622485921,3650190489,4154211501,14243133,ERX10233127,ERS14439192,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.87714,0.88071,0.29319,0.29235,0.69844,0.7164,0.47594,0.47385,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11244,ERR10782549,ERX10233126,ERS14439191,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 3,E MTAB 12503:Sample 3,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 3 p,Sample 3 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz,fastq fastq,13839085674.0,45824787.0,E MTAB 12503:20170530.A 3 R,0:151 1:151,A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362,151,151,,,3812423011,3120168590,3163957945,3729983766,12552362,ERX10233126,ERS14439191,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88987,0.74432,0.33651,0.27875,0.69229,0.72934,0.46981,0.46116,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11747,ERR11608177,ERX11010308,ERS15939662,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU2,SAMEA113945412,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945412|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU2|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU2|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU2 p,MU2 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU2_R1.fastq.gz MU2_R2.fastq.gz,fastq fastq,8373912900.0,27913043.0,E MTAB 13116:MU2 R,0:150 1:150,A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489,150,150,,,2149105370,2028251580,2055193482,2141168979,193489,ERX11010308,ERS15939662,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11748,ERR11608179,ERX11010310,ERS15939664,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT1,SAMEA113945414,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945414|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:WT1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:WT1|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT1 p,WT1 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT1_R1.fastq.gz WT1_R2.fastq.gz,fastq fastq,6729388500.0,22431295.0,E MTAB 13116:WT1 R,0:150 1:150,A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873,150,150,,,1730015872,1621295817,1657133586,1720858352,84873,ERX11010310,ERS15939664,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11749,ERR11608176,ERX11010307,ERS15939661,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU1,SAMEA113945411,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945411|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU1|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU1 p,MU1 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU1_R1.fastq.gz MU1_R2.fastq.gz,fastq fastq,7310352000.0,24367840.0,E MTAB 13116:MU1 R,0:150 1:150,A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432,150,150,,,1888660247,1748082353,1788562372,1884958596,88432,ERX11010307,ERS15939661,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11750,ERR11608178,ERX11010309,ERS15939663,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,MU3,SAMEA113945413,"Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences",ENA first public:2024 07 01|External Id:SAMEA113945413|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU3|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU3|scientific name:Danio rerio|sex:mixed|strain:Tubingen,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:MU3 p,MU3 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,MU3_R1.fastq.gz MU3_R2.fastq.gz,fastq fastq,8826207900.0,29420693.0,E MTAB 13116:MU3 R,0:150 1:150,A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162,150,150,,,2298326835,2100185951,2130807919,2296678033,209162,ERX11010309,ERS15939663,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11751,ERR11608180,ERX11010311,ERS15939665,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT2,E MTAB 13116:WT2,,strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT2 p,WT2 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT2_R1.fastq.gz WT2_R2.fastq.gz,fastq fastq,8368621500.0,27895405.0,E MTAB 13116:WT2 R,0:150 1:150,A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219,150,150,,,2126734187,2050458346,2078646608,2112586140,196219,ERX11010311,ERS15939665,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
11752,ERR11608181,ERX11010312,ERS15939666,ERP148707,PRJEB63561,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E-MTAB-13116,Transcriptome Analysis,Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,,Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,WT3,E MTAB 13116:WT3,,strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27,,,,,,,,,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,E MTAB 13116:WT3 p,WT3 p,RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP148707,Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors,ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01,WT3_R1.fastq.gz WT3_R2.fastq.gz,fastq fastq,8718445500.0,29061485.0,E MTAB 13116:WT3 R,0:150 1:150,A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540,150,150,,,2244668655,2103611849,2135345835,2234609621,209540,ERX11010312,ERS15939666,ERA24542523,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,unknown,bulk,unknown,unknown,,United Kingdom,2023-06-27,Hatching,Embryo,Whole Organism,All anatomical structures
32018,SRR28960817,SRX24490444,SRS21239720,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 2,,strain:wild type|isolate:10|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 2,Empty RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V2_2.fastq.gz C-V2_1.fastq.gz,fastq fastq,4988932790.0,16519645.0,C V2 1.fastq.gz,0:151 1:151,A:1355149914;C:1135513565;G:1149109922;T:1349135360;N:24029,151,151,,,1355149914,1135513565,1149109922,1349135360,24029,SRX24490444,SRS21239720,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94379,0.94549,0.11621,0.11505,0.65423,0.65577,0.48135,0.48232,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32019,SRR28960818,SRX24490443,SRS21239719,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 1,,strain:wild type|isolate:9|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 1,Empty RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V1_2.fastq.gz C-V1_1.fastq.gz,fastq fastq,5032900970.0,16665235.0,C V1 1.fastq.gz,0:151 1:151,A:1378766254;C:1133849186;G:1146563693;T:1373698300;N:23537,151,151,,,1378766254,1133849186,1146563693,1373698300,23537,SRX24490443,SRS21239719,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9444,0.94533,0.11258,0.11038,0.65194,0.65259,0.48812,0.48428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32020,SRR28960819,SRX24490442,SRS21239718,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C4,,strain:wild type|isolate:8|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C4,igldcp C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C4_2.fastq.gz G17-C4_1.fastq.gz,fastq fastq,5008644028.0,16584914.0,G17 C4 1.fastq.gz,0:151 1:151,A:1365541116;C:1135139643;G:1150040618;T:1357899842;N:22809,151,151,,,1365541116,1135139643,1150040618,1357899842,22809,SRX24490442,SRS21239718,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94527,0.94533,0.10689,0.10479,0.65535,0.65681,0.47637,0.48487,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32021,SRR28960820,SRX24490441,SRS21239717,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C3,,strain:wild type|isolate:7|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C3,igldcp C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C3_2.fastq.gz G17-C3_1.fastq.gz,fastq fastq,4980119222.0,16490461.0,G17 C3 1.fastq.gz,0:151 1:151,A:1360303556;C:1126738486;G:1145297479;T:1347756591;N:23110,151,151,,,1360303556,1126738486,1145297479,1347756591,23110,SRX24490441,SRS21239717,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9466,0.94717,0.11289,0.11094,0.66257,0.66464,0.47181,0.47916,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32022,SRR28960821,SRX24490440,SRS21239716,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C2,,strain:wild type|isolate:6|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C2,igldcp C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C2_2.fastq.gz G17-C2_1.fastq.gz,fastq fastq,5007933422.0,16582561.0,G17 C2 1.fastq.gz,0:151 1:151,A:1372213671;C:1129918132;G:1143655284;T:1362122899;N:23436,151,151,,,1372213671,1129918132,1143655284,1362122899,23436,SRX24490440,SRS21239716,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94572,0.94517,0.11003,0.10818,0.65658,0.65805,0.4773,0.48344,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32023,SRR28960822,SRX24490439,SRS21239715,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C1,,strain:wild type|isolate:5|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C1,igldcp C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C1_1.fastq.gz G17-C1_2.fastq.gz,fastq fastq,5024913070.0,16638785.0,G17 C1 1.fastq.gz,0:151 1:151,A:1380366672;C:1129585807;G:1150817244;T:1364119307;N:24040,151,151,,,1380366672,1129585807,1150817244,1364119307,24040,SRX24490439,SRS21239715,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94287,0.94431,0.11558,0.11383,0.65277,0.65382,0.4826,0.48102,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32024,SRR28960823,SRX24490438,SRS21239714,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C4,,strain:wild type|isolate:4|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C4,Empty C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C4_2.fastq.gz C-C4_1.fastq.gz,fastq fastq,4979945874.0,16489887.0,C C4 1.fastq.gz,0:151 1:151,A:1355600042;C:1132041799;G:1147315384;T:1344965018;N:23631,151,151,,,1355600042,1132041799,1147315384,1344965018,23631,SRX24490438,SRS21239714,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94757,0.94857,0.10346,0.10203,0.65539,0.65673,0.4708,0.46117,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32025,SRR28960827,SRX24490437,SRS21239713,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C3,,strain:wild type|isolate:3|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C3,Empty C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C3_2.fastq.gz C-C3_1.fastq.gz,fastq fastq,5029174894.0,16652897.0,C C3 1.fastq.gz,0:151 1:151,A:1374911488;C:1136783068;G:1150269816;T:1367186209;N:24313,151,151,,,1374911488,1136783068,1150269816,1367186209,24313,SRX24490437,SRS21239713,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94336,0.94484,0.11529,0.11371,0.65305,0.65488,0.47386,0.4875,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32026,SRR28960824,SRX24490436,SRS21239712,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 4,,strain:wild type|isolate:15|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 4,igldcp RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V4_1.fastq.gz G17-V4_2.fastq.gz,fastq fastq,5038044634.0,16682267.0,G17 V4 1.fastq.gz,0:151 1:151,A:1373754614;C:1142848550;G:1159235100;T:1362182221;N:24149,151,151,,,1373754614,1142848550,1159235100,1362182221,24149,SRX24490436,SRS21239712,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94236,0.94358,0.10841,0.10623,0.65429,0.65512,0.47952,0.47896,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32027,SRR28960825,SRX24490435,SRS21239711,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 2,,strain:wild type|isolate:14|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 2,igldcp RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V2_2.fastq.gz G17-V2_1.fastq.gz,fastq fastq,4992836442.0,16532571.0,G17 V2 1.fastq.gz,0:151 1:151,A:1370989397;C:1121917932;G:1135482493;T:1364423268;N:23352,151,151,,,1370989397,1121917932,1135482493,1364423268,23352,SRX24490435,SRS21239711,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94244,0.94361,0.11703,0.11517,0.65297,0.65305,0.47906,0.47762,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32028,SRR28960826,SRX24490434,SRS21239710,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 1,,strain:wild type|isolate:13|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 1,igldcp RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V1_2.fastq.gz G17-V1_1.fastq.gz,fastq fastq,5022577402.0,16631051.0,G17 V1 1.fastq.gz,0:151 1:151,A:1373133624;C:1136711402;G:1147351250;T:1365356916;N:24210,151,151,,,1373133624,1136711402,1147351250,1365356916,24210,SRX24490434,SRS21239710,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94548,0.9457,0.11091,0.10876,0.6566,0.65794,0.47672,0.47334,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32029,SRR28960828,SRX24490433,SRS21239709,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 4,,strain:wild type|isolate:12|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 4,Empty RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V4_1.fastq.gz C-V4_2.fastq.gz,fastq fastq,4996580940.0,16544970.0,C V4 1.fastq.gz,0:151 1:151,A:1365771383;C:1129645420;G:1139771568;T:1361369690;N:22879,151,151,,,1365771383,1129645420,1139771568,1361369690,22879,SRX24490433,SRS21239709,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94201,0.94399,0.10865,0.10729,0.65295,0.65397,0.47378,0.48264,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32030,SRR28960829,SRX24490432,SRS21239708,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 3,,strain:wild type|isolate:11|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 3,Empty RGNNV 3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V3_1.fastq.gz C-V3_2.fastq.gz,fastq fastq,4990782540.0,16525770.0,C V3 1.fastq.gz,0:151 1:151,A:1370883963;C:1121960304;G:1139361266;T:1358553278;N:23729,151,151,,,1370883963,1121960304,1139361266,1358553278,23729,SRX24490432,SRS21239708,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94311,0.94426,0.10644,0.10476,0.65535,0.65756,0.46134,0.44955,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32031,SRR28960830,SRX24490431,SRS21239707,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C2,,strain:wild type|isolate:2|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C2,Empty C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C2_2.fastq.gz C-C2_1.fastq.gz,fastq fastq,4991313154.0,16527527.0,C C2 1.fastq.gz,0:151 1:151,A:1366713096;C:1125818845;G:1141236594;T:1357520576;N:24043,151,151,,,1366713096,1125818845,1141236594,1357520576,24043,SRX24490431,SRS21239707,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94263,0.94476,0.10847,0.10745,0.65928,0.65904,0.47366,0.47959,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32032,SRR28960831,SRX24490430,SRS21239702,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C1,,strain:wild type|isolate:1|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C1,Empty C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C1_1.fastq.gz C-C1_2.fastq.gz,fastq fastq,5031068434.0,16659167.0,C C1 1.fastq.gz,0:151 1:151,A:1369231804;C:1143688515;G:1163238884;T:1354885267;N:23964,151,151,,,1369231804,1143688515,1163238884,1354885267,23964,SRX24490430,SRS21239702,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94547,0.94589,0.10958,0.10835,0.6564,0.6565,0.48608,0.48591,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32370,SRR29180530,SRX24700714,SRS21428245,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.,,,,,DES,,isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of DES treated,DES,DES,Sequencing the transcriptomes of zebrafish embryos of DES treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz,fastq fastq,9169560000.0,30565200.0,DES TAAGGC L001 R1 001.fastq.gz,0:150 1:150,A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630,150,150,,,2545096687,2037322055,2024787099,2562124529,229630,SRX24700714,SRS21428245,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
32371,SRR29180531,SRX24700713,SRS21428246,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.,,,,,IOX,,isolate:exposure to IOX|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to IOX|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of IOX treated,IOX,IOX,Sequencing the transcriptomes of zebrafish embryos of IOX treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz,fastq fastq,9547157100.0,31823857.0,IOX CGTACT L001 R1 001.fastq.gz,0:150 1:150,A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429,150,150,,,2631030736,2146265744,2124421595,2645201596,237429,SRX24700713,SRS21428246,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
32372,SRR29180532,SRX24700712,SRS21428244,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.,,,,,CTR,,isolate:control|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of CTR treated,CTR,CTR,Sequencing the transcriptomes of zebrafish embryos of control,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz,fastq fastq,9602954100.0,32009847.0,CTR AGGCAG L001 R1 001.fastq.gz,0:150 1:150,A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825,150,150,,,2637866848,2169057233,2152906664,2642882530,240825,SRX24700712,SRS21428244,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
39756,SRR2125736,SRX1117105,SRS1010315,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,Polr1c2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish Polr1c2|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Polr1c2,RNA Seq of Polr1c2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,Polr1c2_S2_L001_R1_001.fastq.gz Polr1c2_S2_L001_R2_001.fastq.gz,bam fastq,1024040592.0,3467167.0,RNA Seq of Polr1c2,0:147.69 1:147.67,A:280222262;C:231619577;G:229733851;T:282415559;N:49343,147,147,,,280222262,231619577,229733851,282415559,49343,SRX1117105,SRS1010315,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.94843,0.95151,0.09589,0.09554,0.68747,0.68694,0.48798,0.48429,150,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
39757,SRR2125735,SRX1117104,SRS1010314,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,polr1cKO,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of polr1cKO|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of polr1cKO,RNA Seq of polr1cKO,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,polr1cKO_S2_L001_R2_001.fastq.gz polr1cKO_S2_L001_R1_001.fastq.gz,fastq fastq,2153644339.0,7160972.0,RNA Seq of polr1cKO,0:150.40 1:150.34,A:558724957;C:517375772;G:514543839;T:562990605;N:9166,150,150,,,558724957,517375772,514543839,562990605,9166,SRX1117104,SRS1010314,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95998,0.9611,0.07455,0.0729,0.65354,0.65496,0.45853,0.46158,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39758,SRR2125734,SRX1117103,SRS1010313,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,AB2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of AB2|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB2,RNA Seq of AB2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,AB2_S1_L001_R2_001.fastq.gz AB2_S1_L001_R1_001.fastq.gz,fastq fastq,829696252.0,2784590.0,RNA Seq of AB2,0:149.00 1:148.96,A:218353676;C:195998962;G:195017076;T:220297820;N:28718,149,148,,,218353676,195998962,195017076,220297820,28718,SRX1117103,SRS1010313,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96274,0.96494,0.05571,0.05462,0.73588,0.73657,0.48938,0.48219,149,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39759,SRR2125733,SRX1117102,SRS1010312,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,WT,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of WT|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of WT,RNA Seq of WT,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,3020Application ReadForward11Application ReadReverse152,SRP061528,,,wt_S1_L001_R1_001.fastq.gz wt_S1_L001_R2_001.fastq.gz,fastq fastq,1937209279.0,6445507.0,RNA Seq of WT,0:150.30 1:150.25,A:496555264;C:470694471;G:467911055;T:502040892;N:7597,150,150,,,496555264,470694471,467911055,502040892,7597,SRX1117102,SRS1010312,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95931,0.96087,0.06913,0.06787,0.66101,0.66431,0.45529,0.4629,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
39911,SRR2255651,SRX1187765,SRS1056695,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant2|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant2,TRAPPC11 Mutant2,TRAPPC11 Mutant2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,fattyliver2_S6_L001_R1_001.fastq.gz fattyliver2_S6_L001_R2_001.fastq.gz,fastq fastq,836752562.0,5540752.0,TRAPPC11 Mutant2,0:75.54 1:75.48,A:219401421;C:198252489;G:195663968;T:223211242;N:223442,75,75,,,219401421,198252489,195663968,223211242,223442,SRX1187765,SRS1056695,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96204,0.96259,0.05777,0.05527,0.74142,0.74089,0.47566,0.47333,75,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39912,SRR2255629,SRX1187764,SRS1056694,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant1|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant1,TRAPPC11 Mutant1,TRAPPC11 Mutant1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,fattyliver1_S5_L001_R1_001.fastq.gz fattyliver1_S5_L001_R2_001.fastq.gz,fastq fastq,752730180.0,4984563.0,TRAPPC11 Mutant1,0:75.53 1:75.48,A:201453785;C:174638707;G:171041330;T:205386632;N:209726,75,75,,,201453785,174638707,171041330,205386632,209726,SRX1187764,SRS1056694,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95653,0.95631,0.07274,0.06976,0.70573,0.70664,0.49403,0.49925,74,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2015-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39913,SRR2255628,SRX1187763,SRS1056693,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS2|BioSampleModel:Model organism or animal,,,,,,,,,PFOS2,PFOS2,PFOS2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,PFOS2_S4_L001_R1_001.fastq.gz PFOS2_S4_L001_R2_001.fastq.gz,fastq fastq,660339622.0,4372724.0,PFOS2,0:75.53 1:75.48,A:174477377;C:155458423;G:152138367;T:178072878;N:192577,75,75,,,174477377,155458423,152138367,178072878,192577,SRX1187763,SRS1056693,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95841,0.95943,0.06213,0.06061,0.71664,0.71717,0.49605,0.5046,76,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39914,SRR2255627,SRX1187762,SRS1056692,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal,,,,,,,,,PFOS1,PFOS1,PFOS1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz,fastq fastq,791950817.0,5244084.0,PFOS1,0:75.53 1:75.48,A:207476025;C:187690975;G:185784999;T:210781701;N:217117,75,75,,,207476025,187690975,185784999,210781701,217117,SRX1187762,SRS1056692,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96195,0.96213,0.051,0.04857,0.7386,0.73927,0.49669,0.49151,76,53,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39915,SRR2255626,SRX1187761,SRS1056691,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO2|BioSampleModel:Model organism or animal,,,,,,,,,DMSO2,DMSO2,DMSO2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,DMSO2_S2_L001_R1_001.fastq.gz DMSO2_S2_L001_R2_001.fastq.gz,fastq fastq,847975709.0,5615263.0,DMSO2,0:75.53 1:75.48,A:222828293;C:200598370;G:196827420;T:227477582;N:244044,75,75,,,222828293,200598370,196827420,227477582,244044,SRX1187761,SRS1056691,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95825,0.95852,0.06376,0.06156,0.71224,0.71313,0.49629,0.49076,76,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39916,SRR2255625,SRX1187760,SRS1056690,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO1|BioSampleModel:Model organism or animal,,,,,,,,,DMSO1,DMSO1,DMSO1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,1500Application ReadForward11Application ReadReverse76,SRP063370,,,DMSO1_S1_L001_R1_001.fastq.gz DMSO1_S1_L001_R2_001.fastq.gz,fastq fastq,825003413.0,5463030.0,DMSO1,0:75.53 1:75.48,A:217714985;C:193454273;G:192078021;T:221527657;N:228477,75,75,,,217714985,193454273,192078021,221527657,228477,SRX1187760,SRS1056690,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96443,0.9657,0.05205,0.04878,0.76581,0.76465,0.49046,0.47298,76,54,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
42097,SRR5483549,SRX2766898,SRS2151000,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C1 CGATGT L001 R1 001,C1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC1L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C1 CGATGT L001,C1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C1_CGATGT_L001_R1_001.fastq C1_CGATGT_L001_R2_001.fastq C1_CGATGT_L002_R1_001.fastq C1_CGATGT_L002_R2_001.fastq,fastq fastq fastq fastq,1411679200.0,14356543.0,C1 CGATGT L001 R2 001.fastq,,A:371472311;C:327400140;G:335224751;T:377147836;N:434162,,,,,371472311,327400140,335224751,377147836,434162,SRX2766898,SRS2151000,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93533,0.94243,0.07183,0.07215,0.72111,0.72251,0.46894,0.47065,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
42098,SRR5483548,SRX2766897,SRS2150999,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C2 CGATGT L001 R1 001,C2,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC2L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C2 CGATGT L001,C2 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C2_TGACCA_L001_R1_001.fastq C2_TGACCA_L001_R2_001.fastq C2_TGACCA_L002_R1_001.fastq C2_TGACCA_L002_R2_001.fastq,fastq fastq fastq fastq,1242565800.0,12898403.0,C2 TGACCA L001 R1 001.fastq,,A:326022462;C:289113775;G:293830205;T:333244455;N:354903,,,,,326022462,289113775,293830205,333244455,354903,SRX2766897,SRS2150999,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93498,0.94161,0.07112,0.0695,0.72693,0.72717,0.46957,0.48109,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42099,SRR5483547,SRX2766896,SRS2150998,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C4 CGATGT L001 R1 001,C4,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC4L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C4 CGATGT L001,C4 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C4_GCCAAT_L001_R1_001.fastq C4_GCCAAT_L001_R2_001.fastq C4_GCCAAT_L002_R1_001.fastq C4_GCCAAT_L002_R2_001.fastq,fastq fastq fastq fastq,1185823950.0,12152845.0,C4 GCCAAT L001 R2 001.fastq,,A:314615152;C:271806853;G:280914266;T:318186592;N:301087,,,,,314615152,271806853,280914266,318186592,301087,SRX2766896,SRS2150998,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93274,0.94146,0.07722,0.07634,0.7223,0.72358,0.48559,0.48318,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42100,SRR5483546,SRX2766895,SRS2150996,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C5 CGATGT L001 R1 001,C5,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC5L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C5 CGATGT L001,C5 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C5_ACTTGA_L001_R1_001.fastq C5_ACTTGA_L001_R2_001.fastq C5_ACTTGA_L002_R1_001.fastq C5_ACTTGA_L002_R2_001.fastq,fastq fastq fastq fastq,1107911114.0,11470347.0,C5 ACTTGA L001 R1 001.fastq,,A:291142814;C:256111405;G:262122909;T:298258834;N:275152,,,,,291142814,256111405,262122909,298258834,275152,SRX2766895,SRS2150996,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93423,0.94182,0.07555,0.07453,0.72344,0.72579,0.47773,0.47732,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42101,SRR5483545,SRX2766894,SRS2150997,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C6 CGATGT L001 R1 001,C6,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC6L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C6 CGATGT L001,C6 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C6_TAGCTT_L001_R1_001.fastq C6_TAGCTT_L002_R1_001.fastq C6_TAGCTT_L002_R2_001.fastq C6_TAGCTT_L001_R2_001.fastq,fastq fastq fastq fastq,1083109717.0,10884377.0,C6 TAGCTT L001 R2 001.fastq,,A:285687095;C:248867355;G:257309681;T:290972966;N:272620,,,,,285687095,248867355,257309681,290972966,272620,SRX2766894,SRS2150997,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.9312,0.94054,0.07791,0.07785,0.72056,0.72131,0.47439,0.47662,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42102,SRR5483544,SRX2766893,SRS2150995,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C7 CGATGT L001 R1 001,C7,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC7L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C7 CGATGT L001,C7 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C7_CTTGTA_L001_R1_001.fastq C7_CTTGTA_L001_R2_001.fastq C7_CTTGTA_L002_R1_001.fastq C7_CTTGTA_L002_R2_001.fastq,fastq fastq fastq fastq,1085918450.0,11100560.0,C7 CTTGTA L002 R2 001.fastq,,A:285918868;C:249635769;G:259725006;T:290324468;N:314339,,,,,285918868,249635769,259725006,290324468,314339,SRX2766893,SRS2150995,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93539,0.94346,0.06947,0.06884,0.72421,0.72502,0.4671,0.48382,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42103,SRR5483543,SRX2766892,SRS2150994,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C8 CGATGT L001 R1 001,C8,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC8L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C8 CGATGT L001,C8 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C8_AGTTCC_L001_R1_001.fastq C8_AGTTCC_L001_R2_001.fastq C8_AGTTCC_L002_R1_001.fastq C8_AGTTCC_L002_R2_001.fastq,fastq fastq fastq fastq,1073608497.0,11267084.0,C8 AGTTCC L001 R1 001.fastq,,A:281312906;C:246954741;G:257647783;T:287433153;N:259914,,,,,281312906,246954741,257647783,287433153,259914,SRX2766892,SRS2150994,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93523,0.94416,0.0757,0.07511,0.72868,0.72924,0.45926,0.48524,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42104,SRR5483542,SRX2766891,SRS2150993,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M1 CGATGT L001 R1 001,M1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM1L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M1 CGATGT L001,M1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M1_ATCACG_L001_R1_001.fastq M1_ATCACG_L001_R2_001.fastq M1_ATCACG_L002_R1_001.fastq M1_ATCACG_L002_R2_001.fastq,fastq fastq fastq fastq,1076263104.0,11250362.0,M1 ATCACG L001 R1 001.fastq,,A:283920293;C:247496404;G:257418630;T:287117906;N:309871,,,,,283920293,247496404,257418630,287117906,309871,SRX2766891,SRS2150993,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93089,0.93777,0.07725,0.07679,0.72519,0.7264,0.47634,0.48399,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures