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
7952,ERR015568,ERX005928,ERS000087,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,ZF male sample1,SAMEA708829,Wellcome Sanger Institute,Alias:ZF male sample1|Description:RNA extracted from whole male adult zebrafish without xxx|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000087|Sample Name:ERS000087|Sex:male|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male body dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish adult male body mRNA three prime end,Zebrafish gene three prime end pull down for genome annotation,20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.,Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:whole fish without xxx|Experimental Factor: SEX:male,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000263,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation,ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16,3444_8.srf,srf,1012667320.0,6662285.0,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male body dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:262408681;C:234183204;G:228254982;T:271015871;N:16804582,76,76,,,262408681,234183204,228254982,271015871,16804582,ERX005928,ERS000087,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95123,0.96116,0.23163,0.22276,0.77847,0.78648,0.42301,0.43528,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Adult,Adult,Whole Organism,All anatomical structures
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
36278,SRR352486,SRX100938,SRS266977,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq Adult,GSM813764,,source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,3P Seq Adult,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924,mixed gender adults,For adult fish anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,GSM813764,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,1,,GEO Accession:GSM813764,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,360Application ReadForward1,SRP008845,,read name barcode proc directive:ignore,3P_Seq_Adult.fastq,fastq,824962572.0,22915627.0,GSM813764 1,0:36,A:230176177;C:144743199;G:130818857;T:314618483;N:4605856,36,,,,230176177,144743199,130818857,314618483,4605856,SRX100938,SRS266977,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.64306,,0.03985,,0.78102,,0.46237,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Adult,Adult,Whole Organism,All anatomical structures
36368,SRR489481,SRX143558,SRS310279,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Adult,GSM919964,,source name:mixed gender adults|genotype/variation:wild type|tissue:whole adult|development stage:adult,3P Seq Adult,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths the text files contain the following columns : chromosome position strand number of polyA length reads followed by the individual measurements lower bounds on polyA tail length,mixed gender adults,For adult fish anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at 80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:whole adult|developmental stage:adult,GSM919964,GSM919964: 3P Seq Adult; Danio rerio; RNA Seq,GSM919964 1,GSM919964: 3P Seq Adult,1,,GEO Accession:GSM919964,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,360Application ReadForward1,SRP012376,,,,,824962572.0,22915627.0,GSM919964 r1,,,,,,,,,,,,SRX143558,SRS310279,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.58864,,0.03693,,0.77173,,0.45964,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Whole Organism,All anatomical structures
36372,SRR498194,SRX148641,SRS334219,SRP013245,PRJNA167126,The zebrafish embryo as an alternative model for the evaluation of liver toxicity using histopathology and expression profiling,GSE38042,Transcriptome Analysis,The zebrafish is as a powerful vertebrate model system for modeling human disease including liver pathology. In ZFE hepatic responses can be expected post exposure to hepatotoxicants because hepatocytes are present from 36 hpf and at 72 hpf the liver is fully functioning. These characteristics make the whole ZFE an attractive alternative model for compound induced hepatotoxicity screening. Therefore the main objective of this study is to further strengthen the applicability of whole ZFE as an alternative model for hepatotoxicity testing with a special focus on the ability to identify gene expression responses in whole ZFE that are suggestive of hepatotoxicity. Deep sequence technology is applied to assess whether hepatotoxicity specific transcripts that are identified in livers of hepatotoxicant treated adult zebrafish can be detected in whole ZFE as well. Overall design: Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled one sample consists of 15 embryos and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver the other for the whole zebrafish embryo are sequenced.,,,,Whole zebrafish embryo,GSM932885,,source name:Whole zebrafish embryo|tissue:whole embryo|developmental stage:embryo|treatment:exposed for 48h t2 xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodar1 tetracycline and valproic acid,Whole zebrafish embryo,Illumina Genome Analyzer pipeline. Genome build: Ensemble Zv8 Release 59 August 2010. Supplementary files format and content: RPKM,Whole zebrafish embryo,Zebrafish are exposed for 48h ttwo xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodarone tetracycline and valproic acid.,Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled one sample consists of 15 embryos and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver the other for the whole zebrafish embryo are sequenced.,,tissue:whole embryo|developmental stage:embryo|treatment:exposed for 48h t2 xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodar1 tetracycline and valproic acid,GSM932885,GSM932885: Whole zebrafish embryo; Danio rerio; RNA Seq,GSM932885 2,GSM932885: Whole zebrafish embryo,1,,GEO Accession:GSM932885,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1000Application ReadForward11Application ReadReverse51,SRP013245,,,s_1_1_sequence-ZFEPOOL.txt s_1_2_sequence-ZFEPOOL.txt,fastq fastq,914344500.0,9143445.0,GSM932885 r1,0:50 1:50,A:250480963;C:204875422;G:204960559;T:253372716;N:654840,50,50,,,250480963,204875422,204960559,253372716,654840,SRX148641,SRS334219,SRA052989,GEO,"Laboratory for Health Protection Research, National Institute of Public Health and the Environment (RIVM)",2,0.88203,0.88134,0.14191,0.14157,0.6616,0.66166,0.47148,0.47851,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,Netherlands,2012-05-17,Adult,Adult,Whole Organism,All anatomical structures
41599,SRR5084081,SRX2401784,SRS1841772,SRP094690,PRJNA356508,Ikk2 regulates cytokinesis during vertebrate development Trancriptome profiling from the wild type and Ikk2 maternal zygotic mutant zebrafish,GSE90971,Transcriptome Analysis,Purpose: The Ikk2 maternal zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition MBT and post MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow we identified 54 276 transcripts in the embryos at 2 hpf and 4 hpf. RNA seq data confirmed lack of expression of a number of genes in the mutant both prior to and post the MBT including genes linked to angiogenesis skin development cytokinesis innate immunity and cytoskeletonT and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2 with two biologic replicates generated by RNA seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA seq based transcriptome characterization improves analysis of NFkB regulated genes. Overall design: Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,,pubmed:28808254,,Ikk2 4h,GSM2418530,,source name:whole embryo|strain:AB|tissue:whole embryo|genotype/variation:ikk2 / ,Ikk2 4h,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome with ensembl annotation 71 using tophat v2.0.9 Mapped reads fragments per kilobase of transcript per million FPKM was calculated and normalized using cuffdiff Cufflinks v2.1.1 with default parameters. Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample ...,whole embryo,No treatment.,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,strain:AB|tissue:whole embryo|genotype/variation:ikk2 / ,GSM2418530,GSM2418530: Ikk2 4h; Danio rerio; RNA Seq,GSM2418530,,1,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2418530,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP094690,,,HS003-SR-R00112_AC2G1KACXX.RZL036_GTGAAA_L005_R1.fastq.gz,fastq,2542977050.0,50859541.0,GSM2418530 r1,0:50,A:644842984;C:617125767;G:574293502;T:705875322;N:839475,50,,,,644842984,617125767,574293502,705875322,839475,SRX2401784,SRS1841772,SRA501296,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.94003,,0.05173,,0.74846,,0.48228,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2016-12-07,Adult,Adult,Whole Organism,All anatomical structures
41600,SRR5084080,SRX2401783,SRS1841771,SRP094690,PRJNA356508,Ikk2 regulates cytokinesis during vertebrate development Trancriptome profiling from the wild type and Ikk2 maternal zygotic mutant zebrafish,GSE90971,Transcriptome Analysis,Purpose: The Ikk2 maternal zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition MBT and post MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow we identified 54 276 transcripts in the embryos at 2 hpf and 4 hpf. RNA seq data confirmed lack of expression of a number of genes in the mutant both prior to and post the MBT including genes linked to angiogenesis skin development cytokinesis innate immunity and cytoskeletonT and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2 with two biologic replicates generated by RNA seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA seq based transcriptome characterization improves analysis of NFkB regulated genes. Overall design: Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,,pubmed:28808254,,WT 4h,GSM2418529,,source name:whole embryo|strain:AB|tissue:whole embryo|genotype/variation:wild type,WT 4h,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome with ensembl annotation 71 using tophat v2.0.9 Mapped reads fragments per kilobase of transcript per million FPKM was calculated and normalized using cuffdiff Cufflinks v2.1.1 with default parameters. Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample ...,whole embryo,No treatment.,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,strain:AB|tissue:whole embryo|genotype/variation:wild type,GSM2418529,GSM2418529: WT 4h; Danio rerio; RNA Seq,GSM2418529,,1,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2418529,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP094690,,,HS003-SR-R00112_AC2G1KACXX.RZL035_CTTGTA_L005_R1.fastq.gz,fastq,2332518650.0,46650373.0,GSM2418529 r1,0:50,A:592842688;C:565456083;G:529345299;T:644109905;N:764675,50,,,,592842688,565456083,529345299,644109905,764675,SRX2401783,SRS1841771,SRA501296,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.93867,,0.04568,,0.74706,,0.46951,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2016-12-07,Adult,Adult,Whole Organism,All anatomical structures
41601,SRR5084079,SRX2401782,SRS1841770,SRP094690,PRJNA356508,Ikk2 regulates cytokinesis during vertebrate development Trancriptome profiling from the wild type and Ikk2 maternal zygotic mutant zebrafish,GSE90971,Transcriptome Analysis,Purpose: The Ikk2 maternal zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition MBT and post MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow we identified 54 276 transcripts in the embryos at 2 hpf and 4 hpf. RNA seq data confirmed lack of expression of a number of genes in the mutant both prior to and post the MBT including genes linked to angiogenesis skin development cytokinesis innate immunity and cytoskeletonT and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2 with two biologic replicates generated by RNA seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA seq based transcriptome characterization improves analysis of NFkB regulated genes. Overall design: Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,,pubmed:28808254,,Ikk2 2h,GSM2418528,,source name:whole embryo|strain:AB|tissue:whole embryo|genotype/variation:ikk2 / ,Ikk2 2h,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome with ensembl annotation 71 using tophat v2.0.9 Mapped reads fragments per kilobase of transcript per million FPKM was calculated and normalized using cuffdiff Cufflinks v2.1.1 with default parameters. Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample ...,whole embryo,No treatment.,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,strain:AB|tissue:whole embryo|genotype/variation:ikk2 / ,GSM2418528,GSM2418528: Ikk2 2h; Danio rerio; RNA Seq,GSM2418528,,1,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2418528,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP094690,,,HS003-SR-R00112_AC2G1KACXX.RZL034_GCCAAT_L005_R1.fastq.gz,fastq,2599886650.0,51997733.0,GSM2418528 r1,0:50,A:671073263;C:627049298;G:585161091;T:715743575;N:859423,50,,,,671073263,627049298,585161091,715743575,859423,SRX2401782,SRS1841770,SRA501296,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.93765,,0.03452,,0.77041,,0.4773,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2016-12-07,Adult,Adult,Whole Organism,All anatomical structures
41602,SRR5084078,SRX2401781,SRS1841769,SRP094690,PRJNA356508,Ikk2 regulates cytokinesis during vertebrate development Trancriptome profiling from the wild type and Ikk2 maternal zygotic mutant zebrafish,GSE90971,Transcriptome Analysis,Purpose: The Ikk2 maternal zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition MBT and post MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow we identified 54 276 transcripts in the embryos at 2 hpf and 4 hpf. RNA seq data confirmed lack of expression of a number of genes in the mutant both prior to and post the MBT including genes linked to angiogenesis skin development cytokinesis innate immunity and cytoskeletonT and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2 with two biologic replicates generated by RNA seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA seq based transcriptome characterization improves analysis of NFkB regulated genes. Overall design: Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,,pubmed:28808254,,WT 2h,GSM2418527,,source name:whole embryo|strain:AB|tissue:whole embryo|genotype/variation:wild type,WT 2h,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome with ensembl annotation 71 using tophat v2.0.9 Mapped reads fragments per kilobase of transcript per million FPKM was calculated and normalized using cuffdiff Cufflinks v2.1.1 with default parameters. Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample ...,whole embryo,No treatment.,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.,strain:AB|tissue:whole embryo|genotype/variation:wild type,GSM2418527,GSM2418527: WT 2h; Danio rerio; RNA Seq,GSM2418527,,1,Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2418527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP094690,,,HS003-SR-R00112_AC2G1KACXX.RZL033_ACAGTG_L005_R1.fastq.gz,fastq,2403580550.0,48071611.0,GSM2418527 r1,0:50,A:617644095;C:582013099;G:542119274;T:661071874;N:732208,50,,,,617644095,582013099,542119274,661071874,732208,SRX2401781,SRS1841769,SRA501296,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.94015,,0.03248,,0.76968,,0.47083,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2016-12-07,Adult,Adult,Whole Organism,All anatomical structures
42111,SRR5418455,SRX2710003,SRS2101766,SRP103090,PRJNA381761,A Novel Perivascular Cell Population in the Zebrafish Brain,GSE97421,Transcriptome Analysis,Purpose: RNA seq analysis from isolated zebrafish fluorescent granular perithelial FGP cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tgkdrl:mCherry;Tgmrc1a:eGFP. Overall design: Total RNA from isolated FGPs endothelial cells and whole fish.,,pubmed:28395729,,Whole fish,GSM2564303,,source name:Adult fish|strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,Whole fish,Illumina software for base calling. Reads trimmed using trimmomatc and aligned using RNA STAR. Differential RNA expression was quantified by subread featureCounts and tested by DESeq2. Genome build: Zv10 GRCz10 danRer10 Supplementary files format and content: Raw Counts.txt: Tab delimited text file includes the raw counts of the samples. Supplementary files format and content: GFP RFP.txt: Tab delimited text file includes the comparisons between the GFP+ and mCherry/RFP+ cells. Supplementary files format and content: GFP Whole.txt: Tab delimited text file includes the comparisons between the GFP+ and whole fish cells.,Adult fish,,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,GSM2564303,GSM2564303: Whole fish; Danio rerio; RNA Seq,GSM2564303,,1,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2564303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP103090,,,Wholefish_S4Aligned.sortedByCoord.out.bam,bam,6617054018.0,59603220.0,GSM2564303 r1,0:111.02,A:1612417561;C:1114955931;G:1470361768;T:2419301446;N:17312,111,,,,1612417561,1114955931,1470361768,2419301446,17312,SRX2710003,SRS2101766,SRA551687,GEO,"Weinstein Lab, NICHD, NIH",1,0.47105,,0.33842,,0.84869,,0.65108,,151,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-04-05,Adult,Adult,Whole Organism,All anatomical structures
42112,SRR5418456,SRX2710003,SRS2101766,SRP103090,PRJNA381761,A Novel Perivascular Cell Population in the Zebrafish Brain,GSE97421,Transcriptome Analysis,Purpose: RNA seq analysis from isolated zebrafish fluorescent granular perithelial FGP cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tgkdrl:mCherry;Tgmrc1a:eGFP. Overall design: Total RNA from isolated FGPs endothelial cells and whole fish.,,pubmed:28395729,,Whole fish,GSM2564303,,source name:Adult fish|strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,Whole fish,Illumina software for base calling. Reads trimmed using trimmomatc and aligned using RNA STAR. Differential RNA expression was quantified by subread featureCounts and tested by DESeq2. Genome build: Zv10 GRCz10 danRer10 Supplementary files format and content: Raw Counts.txt: Tab delimited text file includes the raw counts of the samples. Supplementary files format and content: GFP RFP.txt: Tab delimited text file includes the comparisons between the GFP+ and mCherry/RFP+ cells. Supplementary files format and content: GFP Whole.txt: Tab delimited text file includes the comparisons between the GFP+ and whole fish cells.,Adult fish,,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,GSM2564303,GSM2564303: Whole fish; Danio rerio; RNA Seq,GSM2564303,,1,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2564303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP103090,,,fish1_S9Aligned.sortedByCoord.out.bam,bam,1377266219.0,11551342.0,GSM2564303 r2,0:59.64 1:59.59,A:425474093;C:262960139;G:267182117;T:421097942;N:551928,59,59,,,425474093,262960139,267182117,421097942,551928,SRX2710003,SRS2101766,SRA551687,GEO,"Weinstein Lab, NICHD, NIH",2,0.83186,0.85133,0.45418,0.46776,0.76366,0.77408,0.66192,0.67192,70,68,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-04-05,Adult,Adult,Whole Organism,All anatomical structures
42113,SRR5418457,SRX2710003,SRS2101766,SRP103090,PRJNA381761,A Novel Perivascular Cell Population in the Zebrafish Brain,GSE97421,Transcriptome Analysis,Purpose: RNA seq analysis from isolated zebrafish fluorescent granular perithelial FGP cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tgkdrl:mCherry;Tgmrc1a:eGFP. Overall design: Total RNA from isolated FGPs endothelial cells and whole fish.,,pubmed:28395729,,Whole fish,GSM2564303,,source name:Adult fish|strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,Whole fish,Illumina software for base calling. Reads trimmed using trimmomatc and aligned using RNA STAR. Differential RNA expression was quantified by subread featureCounts and tested by DESeq2. Genome build: Zv10 GRCz10 danRer10 Supplementary files format and content: Raw Counts.txt: Tab delimited text file includes the raw counts of the samples. Supplementary files format and content: GFP RFP.txt: Tab delimited text file includes the comparisons between the GFP+ and mCherry/RFP+ cells. Supplementary files format and content: GFP Whole.txt: Tab delimited text file includes the comparisons between the GFP+ and whole fish cells.,Adult fish,,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,GSM2564303,GSM2564303: Whole fish; Danio rerio; RNA Seq,GSM2564303,,1,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2564303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP103090,,,fish2_S10Aligned.sortedByCoord.out.bam,bam,1743231497.0,15669069.0,GSM2564303 r3,0:55.66 1:55.60,A:525584635;C:344650225;G:347621333;T:524323321;N:1051983,55,55,,,525584635,344650225,347621333,524323321,1051983,SRX2710003,SRS2101766,SRA551687,GEO,"Weinstein Lab, NICHD, NIH",2,0.8376,0.84959,0.44324,0.4524,0.7585,0.77112,0.67205,0.67177,36,36,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-04-05,Adult,Adult,Whole Organism,All anatomical structures
42114,SRR5418458,SRX2710003,SRS2101766,SRP103090,PRJNA381761,A Novel Perivascular Cell Population in the Zebrafish Brain,GSE97421,Transcriptome Analysis,Purpose: RNA seq analysis from isolated zebrafish fluorescent granular perithelial FGP cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tgkdrl:mCherry;Tgmrc1a:eGFP. Overall design: Total RNA from isolated FGPs endothelial cells and whole fish.,,pubmed:28395729,,Whole fish,GSM2564303,,source name:Adult fish|strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,Whole fish,Illumina software for base calling. Reads trimmed using trimmomatc and aligned using RNA STAR. Differential RNA expression was quantified by subread featureCounts and tested by DESeq2. Genome build: Zv10 GRCz10 danRer10 Supplementary files format and content: Raw Counts.txt: Tab delimited text file includes the raw counts of the samples. Supplementary files format and content: GFP RFP.txt: Tab delimited text file includes the comparisons between the GFP+ and mCherry/RFP+ cells. Supplementary files format and content: GFP Whole.txt: Tab delimited text file includes the comparisons between the GFP+ and whole fish cells.,Adult fish,,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal,GSM2564303,GSM2564303: Whole fish; Danio rerio; RNA Seq,GSM2564303,,1,Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2564303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP103090,,,fish3_S11Aligned.sortedByCoord.out.bam,bam,3238280472.0,29071170.0,GSM2564303 r4,0:55.73 1:55.66,A:1002549336;C:618470058;G:623586789;T:991711923;N:1962366,55,55,,,1002549336,618470058,623586789,991711923,1962366,SRX2710003,SRS2101766,SRA551687,GEO,"Weinstein Lab, NICHD, NIH",2,0.83096,0.84582,0.43645,0.44733,0.75881,0.76771,0.64357,0.65966,46,46,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-04-05,Adult,Adult,Whole Organism,All anatomical structures
49058,SRR7637828,SRX4501382,SRS3622149,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FiberTwo,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut11|BioSampleModel:Model organism or animal,,,,,,,,,Fiber2,FiberTwo,FiberTwo,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,SFb2_20180308_CTCAAT_S41_L002_R1_001.fastq.gz SFb2_20180308_CTCAAT_S41_L002_R2_001.fastq.gz,fastq fastq,10494618988.0,34750394.0,SFb2 20180308 CTCAAT S41 L002 R2 001.fastq.gz,0:151 1:151,A:2756954289;C:2479858860;G:2559922727;T:2697539679;N:343433,151,151,,,2756954289,2479858860,2559922727,2697539679,343433,SRX4501382,SRS3622149,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94475,0.94746,0.03971,0.03937,0.75771,0.76108,0.54085,0.52797,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-08-02,Adult,Adult,Whole Organism,All anatomical structures
49059,SRR7637829,SRX4501381,SRS3622148,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,BeadThree,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut9|BioSampleModel:Model organism or animal,,,,,,,,,Bead3,BeadThree,BeadThree,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,MB3_20180308_CGACTG_S39_L002_R2_001.fastq.gz MB3_20180308_CGACTG_S39_L002_R1_001.fastq.gz,fastq fastq,5583089402.0,18487051.0,MB3 20180308 CGACTG S39 L002 R1 001.fastq.gz,0:151 1:151,A:1460792721;C:1322839967;G:1369668696;T:1429612084;N:175934,151,151,,,1460792721,1322839967,1369668696,1429612084,175934,SRX4501381,SRS3622148,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94237,0.9468,0.04223,0.04177,0.74194,0.74499,0.54818,0.55571,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49060,SRR7637830,SRX4501380,SRS3622147,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FiberOne,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut10|BioSampleModel:Model organism or animal,,,,,,,,,Fiber1,FiberOne,FiberOne,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,SFb1_20180308_CGCATA_S40_L002_R2_001.fastq.gz SFb1_20180308_CGCATA_S40_L002_R1_001.fastq.gz,fastq fastq,7368174860.0,24397930.0,SFb1 20180308 CGCATA S40 L002 R2 001.fastq.gz,0:151 1:151,A:1936361048;C:1742614765;G:1801958963;T:1887001771;N:238313,151,151,,,1936361048,1742614765,1801958963,1887001771,238313,SRX4501380,SRS3622147,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94421,0.94804,0.04014,0.03969,0.75501,0.75775,0.52951,0.54195,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49061,SRR7637831,SRX4501379,SRS3622146,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,ControlTwo,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut2|BioSampleModel:Model organism or animal,,,,,,,,,Control2,ControlTwo,ControlTwo,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,ck2_20180308N_CAGCGT_S80_R2_001.fastq.gz ck2_20180308N_CAGCGT_S80_R1_001.fastq.gz,fastq fastq,9368247776.0,31020688.0,ck2 20180308N CAGCGT S80 R1 001.fastq.gz,0:151 1:151,A:2460392017;C:2207268196;G:2315640897;T:2384916572;N:30094,151,151,,,2460392017,2207268196,2315640897,2384916572,30094,SRX4501379,SRS3622146,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94874,0.81138,0.04085,0.0318,0.74093,0.75442,0.52969,0.52322,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49062,SRR7637832,SRX4501378,SRS3622145,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,ControlThree,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut3|BioSampleModel:Model organism or animal,,,,,,,,,Control3,ControlThree,ControlThree,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,ck3_20180308N_CATACC_S81_R2_001.fastq.gz ck3_20180308N_CATACC_S81_R1_001.fastq.gz,fastq fastq,8156423852.0,27008026.0,ck3 20180308N CATACC S81 R2 001.fastq.gz,0:151 1:151,A:2141586323;C:1928412128;G:2019757092;T:2066642037;N:26272,151,151,,,2141586323,1928412128,2019757092,2066642037,26272,SRX4501378,SRS3622145,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94991,0.80786,0.03753,0.02937,0.743,0.7581,0.52953,0.51767,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49063,SRR7637833,SRX4501377,SRS3622143,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FragmentOne,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut4|BioSampleModel:Model organism or animal,,,,,,,,,Fragment1,FragmentOne,FragmentOne,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,FG1_20180308N_CCAGTT_S82_R1_001.fastq.gz FG1_20180308N_CCAGTT_S82_R2_001.fastq.gz,fastq fastq,10309384268.0,34137034.0,FG1 20180308N CCAGTT S82 R2 001.fastq.gz,0:151 1:151,A:2711920404;C:2428019743;G:2538726593;T:2630683876;N:33652,151,151,,,2711920404,2428019743,2538726593,2630683876,33652,SRX4501377,SRS3622143,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.95319,0.81466,0.0366,0.02838,0.76729,0.78139,0.54501,0.54542,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-08-02,Adult,Adult,Whole Organism,All anatomical structures
49064,SRR7637834,SRX4501376,SRS3622144,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,ControlOne,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut1|BioSampleModel:Model organism or animal,,,,,,,,,Control1,ControlOne,ControlOne,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,ck1_20180308N_CACTTC_S79_R1_001.fastq.gz ck1_20180308N_CACTTC_S79_R2_001.fastq.gz,fastq fastq,8302376526.0,27491313.0,ck1 20180308N CACTTC S79 R1 001.fastq.gz,0:151 1:151,A:2185378613;C:1951420825;G:2049874039;T:2115676173;N:26876,151,151,,,2185378613,1951420825,2049874039,2115676173,26876,SRX4501376,SRS3622144,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.9485,0.80065,0.04239,0.03302,0.74172,0.7567,0.52236,0.53217,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49065,SRR7637835,SRX4501375,SRS3622142,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FiberThree,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut12|BioSampleModel:Model organism or animal,,,,,,,,,Fiber3,FiberThree,FiberThree,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,SFb3_20180308_CTGAGC_S42_L002_R2_001.fastq.gz SFb3_20180308_CTGAGC_S42_L002_R1_001.fastq.gz,fastq fastq,8052778660.0,26664830.0,SFb3 20180308 CTGAGC S42 L002 R2 001.fastq.gz,0:151 1:151,A:2108582357;C:1909439595;G:1976426950;T:2058076799;N:252959,151,151,,,2108582357,1909439595,1976426950,2058076799,252959,SRX4501375,SRS3622142,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94666,0.94941,0.03962,0.0395,0.75408,0.75737,0.52613,0.54345,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49066,SRR7637836,SRX4501374,SRS3622141,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,BeadOne,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut7|BioSampleModel:Model organism or animal,,,,,,,,,Bead1,BeadOne,BeadOne,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,MB1_20180308_CCTCCT_S37_L002_R1_001.fastq.gz MB1_20180308_CCTCCT_S37_L002_R2_001.fastq.gz,fastq fastq,6907591036.0,22872818.0,MB1 20180308 CCTCCT S37 L002 R2 001.fastq.gz,0:151 1:151,A:1796574129;C:1649557969;G:1702822523;T:1758411861;N:224554,151,151,,,1796574129,1649557969,1702822523,1758411861,224554,SRX4501374,SRS3622141,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.94402,0.94831,0.03903,0.03905,0.74444,0.74799,0.55334,0.55731,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49067,SRR7637837,SRX4501373,SRS3622140,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,BeadTwo,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut8|BioSampleModel:Model organism or animal,,,,,,,,,Bead2,BeadTwo,BeadTwo,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,MB2_20180308_CGAACT_S38_L002_R1_001.fastq.gz MB2_20180308_CGAACT_S38_L002_R2_001.fastq.gz,fastq fastq,8790666132.0,29108166.0,MB2 20180308 CGAACT S38 L002 R2 001.fastq.gz,0:151 1:151,A:2308382253;C:2076549882;G:2139570034;T:2265871851;N:292112,151,151,,,2308382253,2076549882,2139570034,2265871851,292112,SRX4501373,SRS3622140,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.9414,0.94541,0.04298,0.04231,0.74162,0.74578,0.54352,0.54266,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49068,SRR7637838,SRX4501372,SRS3622137,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FragmentTwo,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut5|BioSampleModel:Model organism or animal,,,,,,,,,Fragment2,FragmentTwo,FragmentTwo,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,FG2_20180308N_CCGAAG_S83_R1_001.fastq.gz FG2_20180308N_CCGAAG_S83_R2_001.fastq.gz,fastq fastq,9210063196.0,30496898.0,FG2 20180308N CCGAAG S83 R2 001.fastq.gz,0:151 1:151,A:2407480323;C:2183272173;G:2291489636;T:2327790772;N:30292,151,151,,,2407480323,2183272173,2291489636,2327790772,30292,SRX4501372,SRS3622137,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.95304,0.81491,0.03815,0.03093,0.75532,0.7696,0.52024,0.54303,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
49069,SRR7637839,SRX4501371,SRS3622139,SRP156164,PRJNA484127,Danio rerio Raw sequence reads,PRJNA484127,Whole Genome Sequencing,The toxic of MPs on Danio rerio gut.,,,,,FragmentThree,,strain:not collected|age:Adult|sex:pooled male and female|tissue:Gut6|BioSampleModel:Model organism or animal,,,,,,,,,Fragment3,FragmentThree,FragmentThree,Analysis the zebrafish gut DEGs post uptake MPs with different shapes,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP156164,,,FG3_20180308N_CCGTGA_S84_R1_001.fastq.gz FG3_20180308N_CCGTGA_S84_R2_001.fastq.gz,fastq fastq,7568963788.0,25062794.0,FG3 20180308N CCGTGA S84 R1 001.fastq.gz,0:151 1:151,A:1979865584;C:1789546939;G:1882858707;T:1916667688;N:24870,151,151,,,1979865584,1789546939,1882858707,1916667688,24870,SRX4501371,SRS3622139,SRA750253,Nanjing University|School of Environment,Nanjing University,2,0.95309,0.81064,0.03664,0.02853,0.75499,0.77001,0.53024,0.54512,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-09-01,Adult,Adult,Whole Organism,All anatomical structures
58876,SRR11519059,SRX8090404,SRS6457255,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 8h,GSM4467035,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 8h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467035,GSM4467035: zfishRibo0wt 8h; Danio rerio; RNA Seq,GSM4467035,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467035,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_8h.fastq.gz,fastq,2563906360.0,33735610.0,GSM4467035 r1,0:76 1:0,A:590255680;C:624101877;G:608571176;T:740906665;N:70962,76,0,,,590255680,624101877,608571176,740906665,70962,SRX8090404,SRS6457255,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.94866,,0.2361,,0.74771,,0.53846,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58877,SRR11519058,SRX8090403,SRS6457254,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 7h,GSM4467034,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467034,GSM4467034: zfishRibo0wt 7h; Danio rerio; RNA Seq,GSM4467034,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467034,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_7h.fastq.gz,fastq,2491297176.0,32780226.0,GSM4467034 r1,0:76 1:0,A:571076928;C:610953845;G:621275453;T:687921883;N:69067,76,0,,,571076928,610953845,621275453,687921883,69067,SRX8090403,SRS6457254,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.89902,,0.20302,,0.75806,,0.55195,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58878,SRR11519057,SRX8090402,SRS6457252,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 6h,GSM4467033,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467033,GSM4467033: zfishRibo0wt 6h; Danio rerio; RNA Seq,GSM4467033,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467033,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_6h.fastq.gz,fastq,2493888016.0,32814316.0,GSM4467033 r1,0:76 1:0,A:559295503;C:631458142;G:596937380;T:706126363;N:70628,76,0,,,559295503,631458142,596937380,706126363,70628,SRX8090402,SRS6457252,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95152,,0.21188,,0.74221,,0.53579,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58879,SRR11519056,SRX8090401,SRS6457253,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 5h,GSM4467032,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467032,GSM4467032: zfishRibo0wt 5h; Danio rerio; RNA Seq,GSM4467032,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467032,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_5h.fastq.gz,fastq,2863999124.0,37684199.0,GSM4467032 r1,0:76 1:0,A:639720186;C:714899862;G:693238952;T:816060855;N:79269,76,0,,,639720186,714899862,693238952,816060855,79269,SRX8090401,SRS6457253,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95365,,0.16575,,0.73448,,0.54672,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58880,SRR11519055,SRX8090400,SRS6457251,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 4h,GSM4467031,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467031,GSM4467031: zfishRibo0wt 4h; Danio rerio; RNA Seq,GSM4467031,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467031,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_4h.fastq.gz,fastq,2533223184.0,33331884.0,GSM4467031 r1,0:76 1:0,A:569364722;C:632186324;G:613168396;T:718432798;N:70944,76,0,,,569364722,632186324,613168396,718432798,70944,SRX8090400,SRS6457251,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95769,,0.13224,,0.74361,,0.52423,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58881,SRR11519054,SRX8090399,SRS6457250,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 3h,GSM4467030,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467030,GSM4467030: zfishRibo0wt 3h; Danio rerio; RNA Seq,GSM4467030,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467030,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_3h.fastq.gz,fastq,2541195888.0,33436788.0,GSM4467030 r1,0:76 1:0,A:558746776;C:641083540;G:621728982;T:719565542;N:71048,76,0,,,558746776,641083540,621728982,719565542,71048,SRX8090399,SRS6457250,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96383,,0.07472,,0.75911,,0.53085,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58882,SRR11519053,SRX8090398,SRS6457248,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 2h,GSM4467029,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467029,GSM4467029: zfishRibo0wt 2h; Danio rerio; RNA Seq,GSM4467029,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467029,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_2h.fastq.gz,fastq,2547048496.0,33513796.0,GSM4467029 r1,0:76 1:0,A:558670296;C:645907430;G:621049936;T:721349864;N:70970,76,0,,,558670296,645907430,621049936,721349864,70970,SRX8090398,SRS6457248,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96389,,0.07455,,0.76,,0.5204,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58883,SRR11519052,SRX8090397,SRS6457249,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 1h,GSM4467028,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 1h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467028,GSM4467028: zfishRibo0wt 1h; Danio rerio; RNA Seq,GSM4467028,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467028,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_1h.fastq.gz,fastq,2275344240.0,29938740.0,GSM4467028 r1,0:76 1:0,A:500070609;C:581032656;G:552335537;T:641843953;N:61485,76,0,,,500070609,581032656,552335537,641843953,61485,SRX8090397,SRS6457249,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96342,,0.07649,,0.75875,,0.52233,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58884,SRR11519051,SRX8090396,SRS6457247,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 0h,GSM4467027,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 0h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467027,GSM4467027: zfishRibo0wt 0h; Danio rerio; RNA Seq,GSM4467027,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_0h.fastq.gz,fastq,2501315724.0,32912049.0,GSM4467027 r1,0:76 1:0,A:558030973;C:625466039;G:640038484;T:677712201;N:68027,76,0,,,558030973,625466039,640038484,677712201,68027,SRX8090396,SRS6457247,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.89966,,0.07039,,0.76067,,0.53601,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58885,SRR11519050,SRX8090395,SRS6457246,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 8h,GSM4467026,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 8h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:poly A capture,GSM4467026,GSM4467026: zfishPolyAwt 8h; Danio rerio; RNA Seq,GSM4467026,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_8h.fastq.gz,fastq,2429894268.0,31972293.0,GSM4467026 r1,0:76 1:0,A:584937045;C:568630282;G:592436865;T:683842155;N:47921,76,0,,,584937045,568630282,592436865,683842155,47921,SRX8090395,SRS6457246,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95736,,0.15618,,0.75418,,0.52643,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58886,SRR11519049,SRX8090394,SRS6457244,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 7h,GSM4467025,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:poly A capture,GSM4467025,GSM4467025: zfishPolyAwt 7h; Danio rerio; RNA Seq,GSM4467025,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_7h.fastq.gz,fastq,2281973188.0,30025963.0,GSM4467025 r1,0:76 1:0,A:516000892;C:564004239;G:579333444;T:622588743;N:45870,76,0,,,516000892,564004239,579333444,622588743,45870,SRX8090394,SRS6457244,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95915,,0.16556,,0.76386,,0.55386,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58887,SRR11519048,SRX8090393,SRS6457245,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 6h,GSM4467024,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:poly A capture,GSM4467024,GSM4467024: zfishPolyAwt 6h; Danio rerio; RNA Seq,GSM4467024,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_6h.fastq.gz,fastq,2454586516.0,32297191.0,GSM4467024 r1,0:76 1:0,A:567790148;C:604134902;G:616413817;T:666199328;N:48321,76,0,,,567790148,604134902,616413817,666199328,48321,SRX8090393,SRS6457245,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96147,,0.15865,,0.75818,,0.54565,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58888,SRR11519047,SRX8090392,SRS6457243,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 5h,GSM4467023,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:poly A capture,GSM4467023,GSM4467023: zfishPolyAwt 5h; Danio rerio; RNA Seq,GSM4467023,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_5h.fastq.gz,fastq,2380658352.0,31324452.0,GSM4467023 r1,0:76 1:0,A:550918628;C:580438305;G:597695173;T:651558275;N:47971,76,0,,,550918628,580438305,597695173,651558275,47971,SRX8090392,SRS6457243,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95989,,0.13789,,0.74341,,0.53449,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58889,SRR11519046,SRX8090391,SRS6457242,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 4h,GSM4467022,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:poly A capture,GSM4467022,GSM4467022: zfishPolyAwt 4h; Danio rerio; RNA Seq,GSM4467022,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_4h.fastq.gz,fastq,2502092216.0,32922266.0,GSM4467022 r1,0:76 1:0,A:548423476;C:643758588;G:642975850;T:666884976;N:49326,76,0,,,548423476,643758588,642975850,666884976,49326,SRX8090391,SRS6457242,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96016,,0.13161,,0.75891,,0.55871,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58890,SRR11519045,SRX8090390,SRS6457241,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 3h,GSM4467021,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:poly A capture,GSM4467021,GSM4467021: zfishPolyAwt 3h; Danio rerio; RNA Seq,GSM4467021,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_3h.fastq.gz,fastq,2608496776.0,34322326.0,GSM4467021 r1,0:76 1:0,A:571388906;C:671364625;G:682368179;T:683322566;N:52500,76,0,,,571388906,671364625,682368179,683322566,52500,SRX8090390,SRS6457241,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96969,,0.15298,,0.78098,,0.56768,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58891,SRR11519044,SRX8090389,SRS6457240,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 2h,GSM4467020,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:poly A capture,GSM4467020,GSM4467020: zfishPolyAwt 2h; Danio rerio; RNA Seq,GSM4467020,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_2h.fastq.gz,fastq,2260403400.0,29742150.0,GSM4467020 r1,0:76 1:0,A:522189473;C:552060968;G:566138267;T:619970621;N:44071,76,0,,,522189473,552060968,566138267,619970621,44071,SRX8090389,SRS6457240,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96297,,0.08765,,0.78399,,0.5331,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58892,SRR11519043,SRX8090388,SRS6457239,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 1h,GSM4467019,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 1h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:poly A capture,GSM4467019,GSM4467019: zfishPolyAwt 1h; Danio rerio; RNA Seq,GSM4467019,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_1h.fastq.gz,fastq,2028859368.0,26695518.0,GSM4467019 r1,0:76 1:0,A:459973220;C:509741356;G:517627384;T:541479126;N:38282,76,0,,,459973220,509741356,517627384,541479126,38282,SRX8090388,SRS6457239,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96767,,0.10368,,0.81858,,0.54455,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58893,SRR11519042,SRX8090387,SRS6457238,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 0h,GSM4467018,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 0h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:poly A capture,GSM4467018,GSM4467018: zfishPolyAwt 0h; Danio rerio; RNA Seq,GSM4467018,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_0h.fastq.gz,fastq,2169902904.0,28551354.0,GSM4467018 r1,0:76 1:0,A:474038869;C:559780620;G:574573413;T:561466815;N:43187,76,0,,,474038869,559780620,574573413,561466815,43187,SRX8090387,SRS6457238,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96674,,0.163,,0.82217,,0.613,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58894,SRR11519041,SRX8090386,SRS6457237,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 7h,GSM4467017,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467017,GSM4467017: TreatedAamanitin zfishPolyAalpha 7h; Danio rerio; RNA Seq,GSM4467017,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_7h.fastq.gz,fastq,2361788996.0,31076171.0,GSM4467017 r1,0:76 1:0,A:550131486;C:580761959;G:573878255;T:656632345;N:384951,76,0,,,550131486,580761959,573878255,656632345,384951,SRX8090386,SRS6457237,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96384,,0.06318,,0.79511,,0.51195,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58895,SRR11519040,SRX8090385,SRS6457236,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 7.5h,GSM4467016,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 7.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467016,GSM4467016: TreatedAamanitin zfishPolyAalpha 7.5h; Danio rerio; RNA Seq,GSM4467016,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467016,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_7.5h.fastq.gz,fastq,2405402204.0,31650029.0,GSM4467016 r1,0:76 1:0,A:529762191;C:612570337;G:631609968;T:631055682;N:404026,76,0,,,529762191,612570337,631609968,631055682,404026,SRX8090385,SRS6457236,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.9627,,0.13637,,0.80726,,0.55163,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58896,SRR11519039,SRX8090384,SRS6457234,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 6h,GSM4467015,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467015,GSM4467015: TreatedAamanitin zfishPolyAalpha 6h; Danio rerio; RNA Seq,GSM4467015,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467015,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_6h.fastq.gz,fastq,2482330696.0,32662246.0,GSM4467015 r1,0:76 1:0,A:568483604;C:615759760;G:619464491;T:678208852;N:413989,76,0,,,568483604,615759760,619464491,678208852,413989,SRX8090384,SRS6457234,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.9624,,0.08888,,0.79105,,0.52285,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58897,SRR11519038,SRX8090383,SRS6457235,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 6.5h,GSM4467014,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 6.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467014,GSM4467014: TreatedAamanitin zfishPolyAalpha 6.5h; Danio rerio; RNA Seq,GSM4467014,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467014,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_6.5h.fastq.gz,fastq,2637121340.0,34698965.0,GSM4467014 r1,0:76 1:0,A:607991115;C:648768142;G:648963472;T:730955221;N:443390,76,0,,,607991115,648768142,648963472,730955221,443390,SRX8090383,SRS6457235,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96223,,0.05876,,0.78693,,0.51118,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58898,SRR11519037,SRX8090382,SRS6457233,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 5h,GSM4467013,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467013,GSM4467013: TreatedAamanitin zfishPolyAalpha 5h; Danio rerio; RNA Seq,GSM4467013,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467013,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_5h.fastq.gz,fastq,2488582152.0,32744502.0,GSM4467013 r1,0:76 1:0,A:569517166;C:606998078;G:629019285;T:682632018;N:415605,76,0,,,569517166,606998078,629019285,682632018,415605,SRX8090382,SRS6457233,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96455,,0.0816,,0.77991,,0.53634,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58899,SRR11519036,SRX8090381,SRS6457232,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 5.5h,GSM4467012,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 5.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467012,GSM4467012: TreatedAamanitin zfishPolyAalpha 5.5h; Danio rerio; RNA Seq,GSM4467012,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_5.5h.fastq.gz,fastq,2425602320.0,31915820.0,GSM4467012 r1,0:76 1:0,A:536016829;C:611729182;G:629092064;T:648359281;N:404964,76,0,,,536016829,611729182,629092064,648359281,404964,SRX8090381,SRS6457232,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96886,,0.1261,,0.79448,,0.57531,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58900,SRR11519035,SRX8090380,SRS6457230,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 4h,GSM4467011,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467011,GSM4467011: TreatedAamanitin zfishPolyAalpha 4h; Danio rerio; RNA Seq,GSM4467011,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_4h.fastq.gz,fastq,2373912972.0,31235697.0,GSM4467011 r1,0:76 1:0,A:569897416;C:557100774;G:583613577;T:662902355;N:398850,76,0,,,569897416,557100774,583613577,662902355,398850,SRX8090380,SRS6457230,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95642,,0.0677,,0.76345,,0.52714,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58901,SRR11519034,SRX8090379,SRS6457231,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 4.5h,GSM4467010,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 4.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467010,GSM4467010: TreatedAamanitin zfishPolyAalpha 4.5h; Danio rerio; RNA Seq,GSM4467010,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_4.5h.fastq.gz,fastq,2546367536.0,33504836.0,GSM4467010 r1,0:76 1:0,A:590944153;C:611757423;G:635042837;T:708195614;N:427509,76,0,,,590944153,611757423,635042837,708195614,427509,SRX8090379,SRS6457231,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96201,,0.06212,,0.76796,,0.51597,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58902,SRR11519033,SRX8090378,SRS6457229,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 3h,GSM4467009,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467009,GSM4467009: TreatedAamanitin zfishPolyAalpha 3h; Danio rerio; RNA Seq,GSM4467009,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_3h.fastq.gz,fastq,1948147824.0,25633524.0,GSM4467009 r1,0:76 1:0,A:457244322;C:470380368;G:477864112;T:542349043;N:309979,76,0,,,457244322,470380368,477864112,542349043,309979,SRX8090378,SRS6457229,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95922,,0.062,,0.7654,,0.51597,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58903,SRR11519032,SRX8090377,SRS6457227,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 3.5h,GSM4467008,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 3.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467008,GSM4467008: TreatedAamanitin zfishPolyAalpha 3.5h; Danio rerio; RNA Seq,GSM4467008,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467008,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_3.5h.fastq.gz,fastq,2227727048.0,29312198.0,GSM4467008 r1,0:76 1:0,A:527821645;C:534611304;G:542982010;T:621939292;N:372797,76,0,,,527821645,534611304,542982010,621939292,372797,SRX8090377,SRS6457227,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95504,,0.0734,,0.76195,,0.52369,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58904,SRR11519031,SRX8090376,SRS6457228,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 2h,GSM4467007,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467007,GSM4467007: TreatedAamanitin zfishPolyAalpha 2h; Danio rerio; RNA Seq,GSM4467007,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467007,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_2h.fastq.gz,fastq,2433943624.0,32025574.0,GSM4467007 r1,0:76 1:0,A:584104490;C:574542508;G:593162776;T:681731342;N:402508,76,0,,,584104490,574542508,593162776,681731342,402508,SRX8090376,SRS6457228,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95487,,0.07062,,0.7737,,0.52084,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58905,SRR11519030,SRX8090375,SRS6457226,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also we sequenced embryos using poly A capture that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 2.5h,GSM4467006,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 2.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467006,GSM4467006: TreatedAamanitin zfishPolyAalpha 2.5h; Danio rerio; RNA Seq,GSM4467006,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467006,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_2.5h.fastq.gz,fastq,2366850900.0,31142775.0,GSM4467006 r1,0:76 1:0,A:568200471;C:563625483;G:574695892;T:659934763;N:394291,76,0,,,568200471,563625483,574695892,659934763,394291,SRX8090375,SRS6457226,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95458,,0.07207,,0.76824,,0.5319,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
61704,SRR12967078,SRX9419617,SRS7634954,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry hypoxia 3,GSM4876604,,source name:Fry|treatment:Hypoxia|tissue:whole organism|generation:F1,RNA seq fry hypoxia 3,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:Hypoxia|tissue:whole organism|generation:F1,GSM4876604,GSM4876604: RNA seq fry hypoxia 3; Danio rerio; RNA Seq,GSM4876604,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876604,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_hypoxia_3.fastq.gz,fastq,1831043500.0,18310435.0,GSM4876604 r1,0:100,A:453592946;C:448115464;G:435517828;T:493810537;N:6725,100,,,,453592946,448115464,435517828,493810537,6725,SRX9419617,SRS7634954,SRA1152608,GEO,"Anatomy, University of Otago",1,0.95654,,0.04261,,0.68943,,0.48196,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
61705,SRR12967077,SRX9419616,SRS7634950,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry hypoxia 2,GSM4876603,,source name:Fry|treatment:Hypoxia|tissue:whole organism|generation:F1,RNA seq fry hypoxia 2,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:Hypoxia|tissue:whole organism|generation:F1,GSM4876603,GSM4876603: RNA seq fry hypoxia 2; Danio rerio; RNA Seq,GSM4876603,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876603,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_hypoxia_2.fastq.gz,fastq,1697033700.0,16970337.0,GSM4876603 r1,0:100,A:423260271;C:414551737;G:400905796;T:458309500;N:6396,100,,,,423260271,414551737,400905796,458309500,6396,SRX9419616,SRS7634950,SRA1152608,GEO,"Anatomy, University of Otago",1,0.95697,,0.0454,,0.68018,,0.46784,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
61706,SRR12967076,SRX9419615,SRS7634952,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry hypoxia 1,GSM4876602,,source name:Fry|treatment:Hypoxia|tissue:whole organism|generation:F1,RNA seq fry hypoxia 1,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:Hypoxia|tissue:whole organism|generation:F1,GSM4876602,GSM4876602: RNA seq fry hypoxia 1; Danio rerio; RNA Seq,GSM4876602,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876602,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_hypoxia_1.fastq.gz,fastq,1869090700.0,18690907.0,GSM4876602 r1,0:100,A:459749839;C:460580178;G:447762245;T:500991209;N:7229,100,,,,459749839,460580178,447762245,500991209,7229,SRX9419615,SRS7634952,SRA1152608,GEO,"Anatomy, University of Otago",1,0.96222,,0.04095,,0.69264,,0.47579,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
61707,SRR12967075,SRX9419614,SRS7634951,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry no treatment 3,GSM4876601,,source name:Fry|treatment:No treatment|tissue:whole organism|generation:F1,RNA seq fry no treatment 3,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:No treatment|tissue:whole organism|generation:F1,GSM4876601,GSM4876601: RNA seq fry no treatment 3; Danio rerio; RNA Seq,GSM4876601,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876601,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_no_treatment_3.fastq.gz,fastq,1884228500.0,18842285.0,GSM4876601 r1,0:100,A:458973216;C:466296369;G:453933767;T:505018258;N:6890,100,,,,458973216,466296369,453933767,505018258,6890,SRX9419614,SRS7634951,SRA1152608,GEO,"Anatomy, University of Otago",1,0.95707,,0.03637,,0.69321,,0.45801,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
61708,SRR12967074,SRX9419613,SRS7634949,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry no treatment 2,GSM4876600,,source name:Fry|treatment:No treatment|tissue:whole organism|generation:F1,RNA seq fry no treatment 2,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:No treatment|tissue:whole organism|generation:F1,GSM4876600,GSM4876600: RNA seq fry no treatment 2; Danio rerio; RNA Seq,GSM4876600,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876600,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_no_treatment_2.fastq.gz,fastq,1743456500.0,17434565.0,GSM4876600 r1,0:100,A:427368173;C:431477027;G:416719159;T:467885635;N:6506,100,,,,427368173,431477027,416719159,467885635,6506,SRX9419613,SRS7634949,SRA1152608,GEO,"Anatomy, University of Otago",1,0.96131,,0.03586,,0.69656,,0.46853,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
61709,SRR12967073,SRX9419611,SRS7634948,SRP290840,PRJNA673886,Paternal hypoxia exposure primes offspring for increased hypoxia resistance,GSE160662,Other,Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.,,pubmed:36038899,,RNA seq fry no treatment 1,GSM4876599,,source name:Fry|treatment:No treatment|tissue:whole organism|generation:F1,RNA seq fry no treatment 1,Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.,Fry,In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.,treatment:No treatment|tissue:whole organism|generation:F1,GSM4876599,GSM4876599: RNA seq fry no treatment 1; Danio rerio; RNA Seq,GSM4876599,,1,Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.,GEO Accession:GSM4876599,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP290840,,,RNA_seq_fry_no_treatment_1.fastq.gz,fastq,1996165600.0,19961656.0,GSM4876599 r1,0:100,A:489777705;C:492746137;G:478910532;T:534723587;N:7639,100,,,,489777705,492746137,478910532,534723587,7639,SRX9419611,SRS7634948,SRA1152608,GEO,"Anatomy, University of Otago",1,0.95819,,0.03758,,0.70151,,0.46991,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2020-11-02,Undetermined,Adult,Whole Organism,All anatomical structures
62475,SRR13221789,SRX9654237,SRS7853434,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,LKO2,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:LAL KO|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,LKO2,LKO2,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,LKO2_R1.fastq.gz LKO2_R2.fastq.gz,fastq fastq,6036272700.0,20120909.0,LKO2 R1.fastq.gz,0:150 1:150,A:1601206536;C:1418087701;G:1426655325;T:1590179237;N:143901,150,150,,,1601206536,1418087701,1426655325,1590179237,143901,SRX9654237,SRS7853434,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.94664,0.94241,0.07651,0.07615,0.6608,0.66567,0.45863,0.4577,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62476,SRR13221790,SRX9654236,SRS7853433,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,LKO1,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:lal knockout|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,LKO1,LKO1,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,LKO1_R1.fastq.gz LKO1_R2.fastq.gz,fastq fastq,6640716000.0,22135720.0,LKO1 R1.fastq.gz,0:150 1:150,A:1756949709;C:1564569001;G:1580752460;T:1738424371;N:20459,150,150,,,1756949709,1564569001,1580752460,1738424371,20459,SRX9654236,SRS7853433,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.95033,0.94458,0.07707,0.07686,0.65835,0.6591,0.47143,0.47082,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62477,SRR13221791,SRX9654235,SRS7853432,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,WT2L,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:Wildtype|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,WT2L,WT2L,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,WT2L_R1.fastq.gz WT2L_R2.fastq.gz,fastq fastq,6956682300.0,23188941.0,WT2L R1.fastq.gz,0:150 1:150,A:1840614101;C:1638232524;G:1657443860;T:1820370318;N:21497,150,150,,,1840614101,1638232524,1657443860,1820370318,21497,SRX9654235,SRS7853432,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.95135,0.94558,0.07516,0.07485,0.66403,0.66505,0.47807,0.47628,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62478,SRR13221792,SRX9654234,SRS7853431,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,WT1L,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:WT|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,WT1L,WT1L,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,WT1L_R1.fastq.gz WT1L_R2.fastq.gz,fastq fastq,6656937600.0,22189792.0,WT1L R1.fastq.gz,0:150 1:150,A:1774798990;C:1555136438;G:1570885194;T:1756096008;N:20970,150,150,,,1774798990,1555136438,1570885194,1756096008,20970,SRX9654234,SRS7853431,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.94852,0.94252,0.09019,0.0895,0.65374,0.6546,0.46386,0.46519,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62479,SRR13221793,SRX9654233,SRS7853430,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,AKO2,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:Atgl KO|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,AKO2,AKO2,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,AKO2_R1.fastq.gz AKO2_R2.fastq.gz,fastq fastq,7159005600.0,23863352.0,AKO2 R1.fastq.gz,0:150 1:150,A:1899574066;C:1686063701;G:1700099039;T:1873246610;N:22184,150,150,,,1899574066,1686063701,1700099039,1873246610,22184,SRX9654233,SRS7853430,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.94503,0.94035,0.07309,0.07271,0.66699,0.66691,0.49612,0.50397,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62480,SRR13221794,SRX9654232,SRS7853429,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,AKO1,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:atgl knockout|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,AKO1,AKO1,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,AKO1_R1.fastq.gz AKO1_R2.fastq.gz,fastq fastq,6731721000.0,22439070.0,AKO1 R1.fastq.gz,0:150 1:150,A:1745882460;C:1610945656;G:1625370653;T:1749501333;N:20898,150,150,,,1745882460,1610945656,1625370653,1749501333,20898,SRX9654232,SRS7853429,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.93222,0.93219,0.02488,0.02484,0.71652,0.71612,0.47921,0.47343,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62481,SRR13221795,SRX9654231,SRS7853428,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,WT2,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:wildtype|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,WT2,WT2,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,WT2_R1.fastq.gz WT2_R2.fastq.gz,fastq fastq,6119265600.0,20397552.0,WT2 R1.fastq.gz,0:150 1:150,A:1619238473;C:1443680669;G:1457083041;T:1599244276;N:19141,150,150,,,1619238473,1443680669,1457083041,1599244276,19141,SRX9654231,SRS7853428,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.94166,0.93671,0.06976,0.06929,0.68635,0.68807,0.49396,0.49711,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
62482,SRR13221796,SRX9654230,SRS7853427,SRP297176,PRJNA683669,Transcriptional regulation of AKO and LKO in zebrafish.,PRJNA683669,Other,The RNA for sequencing was collected from six RNA samples per treatment WT/AKO and WT/LKO male zebrafish.,,,,,WT1,,breed:zebrafish|age:4 mpf|sex:male|tissue:whole fish|genotype:wt|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,WT1,WT1,Transcriptome sequencing was conducted by using Illumina HiSeq 2500 according to the manufacturer's instructions. post filtering out low quality reads the remaining clean reads were assembled and mapped to the zebrafish reference genome.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP297176,,,WT1_R1.fastq.gz WT1_R2.fastq.gz,fastq fastq,7607982300.0,25359941.0,WT1 R1.fastq.gz,0:150 1:150,A:1998356357;C:1800668862;G:1820187726;T:1988746210;N:23145,150,150,,,1998356357,1800668862,1820187726,1988746210,23145,SRX9654230,SRS7853427,SRA1169092,"LANEH|School of Life Sciences, East China Normal Univers",LANEH,2,0.94407,0.93934,0.06239,0.06217,0.69404,0.69522,0.53015,0.52721,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Unknown,2020-12-09,Adult,Adult,Whole Organism,All anatomical structures
64538,SRR14915030,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_1_1.fq.gz Zebrafish_3m_COL64_1_2.fq.gz,fastq fastq,3509355300.0,23395702.0,GSM5400025 r1,0:150 1:150,A:1033838372;C:621125453;G:637527732;T:1213662404;N:3201339,150,150,,,1033838372,621125453,637527732,1213662404,3201339,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36321,,0.02305,,0.82554,,0.50827,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64539,SRR14915031,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_2_1.fq.gz Zebrafish_3m_COL64_2_2.fq.gz,fastq fastq,1665060900.0,11100406.0,GSM5400025 r2,0:150 1:150,A:462369470;C:317060096;G:327014453;T:557786784;N:830097,150,150,,,462369470,317060096,327014453,557786784,830097,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.13839,,0.00808,,0.91569,,0.53255,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64540,SRR14915032,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_3_1.fq.gz Zebrafish_3m_COL64_3_2.fq.gz,fastq fastq,2150244600.0,14334964.0,GSM5400025 r3,0:150 1:150,A:601841098;C:403651653;G:418726941;T:723163387;N:2861521,150,150,,,601841098,403651653,418726941,723163387,2861521,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.14947,,0.00856,,0.91563,,0.52901,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64541,SRR14915033,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_4_1.fq.gz Zebrafish_3m_COL64_4_2.fq.gz,fastq fastq,2197416600.0,14649444.0,GSM5400025 r4,0:150 1:150,A:623049639;C:408736499;G:423211202;T:740201304;N:2217956,150,150,,,623049639,408736499,423211202,740201304,2217956,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.31503,,0.01599,,0.86805,,0.52639,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64542,SRR14915034,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_5_1.fq.gz Zebrafish_3m_COL64_5_2.fq.gz,fastq fastq,15591467400.0,103943116.0,GSM5400025 r5,0:150 1:150,A:4293072963;C:3172864759;G:3328412245;T:4775949229;N:21168204,150,150,,,4293072963,3172864759,3328412245,4775949229,21168204,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.42792,,0.02171,,0.85798,,0.53122,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64543,SRR14915035,SRX11229465,SRS9283357,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL64,GSM5400025,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL64,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400025,GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq,GSM5400025,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL64_6_1.fq.gz Zebrafish_3m_COL64_6_2.fq.gz,fastq fastq,12549507270.0,144247210.0,GSM5400025 r6,0:24 1:150,A:4029002995;C:2554410310;G:2623555177;T:3319223578;N:23315210,24,150,,,4029002995,2554410310,2623555177,3319223578,23315210,SRX11229465,SRS9283357,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38859,,0.01815,,0.85269,,0.5308,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64544,SRR14915024,SRX11229464,SRS9283356,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL63,GSM5400024,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL63,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400024,GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq,GSM5400024,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL63_1_1.fq.gz Zebrafish_3m_COL63_1_2.fq.gz,fastq fastq,2055042600.0,13700284.0,GSM5400024 r1,0:150 1:150,A:611481772;C:368434834;G:377372486;T:695791152;N:1962356,150,150,,,611481772,368434834,377372486,695791152,1962356,SRX11229464,SRS9283356,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34483,,0.02058,,0.82974,,0.52413,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64545,SRR14915025,SRX11229464,SRS9283356,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL63,GSM5400024,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL63,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400024,GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq,GSM5400024,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL63_2_1.fq.gz Zebrafish_3m_COL63_2_2.fq.gz,fastq fastq,160975800.0,1073172.0,GSM5400024 r2,0:150 1:150,A:44979062;C:31715522;G:32816505;T:51394061;N:70650,150,150,,,44979062,31715522,32816505,51394061,70650,SRX11229464,SRS9283356,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.14018,,0.00811,,0.91565,,0.53293,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64546,SRR14915026,SRX11229464,SRS9283356,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL63,GSM5400024,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL63,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400024,GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq,GSM5400024,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL63_3_1.fq.gz Zebrafish_3m_COL63_3_2.fq.gz,fastq fastq,948599100.0,6323994.0,GSM5400024 r3,0:150 1:150,A:270719772;C:179859378;G:186167273;T:310493229;N:1359448,150,150,,,270719772,179859378,186167273,310493229,1359448,SRX11229464,SRS9283356,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.15861,,0.00833,,0.90536,,0.53615,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures
64547,SRR14915027,SRX11229464,SRS9283356,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 3m COL63,GSM5400024,,source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism,Microwell seq datasets of Zebrafish 3m COL63,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 3m sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:3 month 90 day|tissue:whole organism,GSM5400024,GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq,GSM5400024,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,,Zebrafish_3m_COL63_4_1.fq.gz Zebrafish_3m_COL63_4_2.fq.gz,fastq fastq,1296727200.0,8644848.0,GSM5400024 r4,0:150 1:150,A:373182160;C:244740194;G:252531468;T:424978804;N:1294574,150,150,,,373182160,244740194,252531468,424978804,1294574,SRX11229464,SRS9283356,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.30429,,0.0152,,0.86466,,0.53074,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-06-25,Adult,Adult,Whole Organism,All anatomical structures