rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
32,DRR408242,DRX393848,DRS407006,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 3,zebrafish adult gut replicate 3,SAMD00529462,,sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529462,DRX393848,AR019 gut 6 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529462,,,,3546347364.0,28145614.0,DRR408242,0:126 1:0,A:919466631;C:829424335;G:818581155;T:978810217;N:65026,126,0,,,919466631,829424335,818581155,978810217,65026,DRX393848,DRS407006,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
33,DRR408241,DRX393847,DRS407005,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 2,zebrafish adult gut replicate 2,SAMD00529461,,sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529461,DRX393847,AR006 gut 4 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529461,,,,3671973648.0,29142648.0,DRR408241,0:126 1:0,A:942167543;C:859431290;G:852661772;T:1017643011;N:70032,126,0,,,942167543,859431290,852661772,1017643011,70032,DRX393847,DRS407005,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
34,DRR408240,DRX393846,DRS407004,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 1,zebrafish adult gut replicate 1,SAMD00529460,,sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529460,DRX393846,AR004 gut 2 adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529460,,,,3480523704.0,27623204.0,DRR408240,0:126 1:0,A:898051986;C:827557593;G:816541244;T:938307607;N:65274,126,0,,,898051986,827557593,816541244,938307607,65274,DRX393846,DRS407004,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
35,DRR408239,DRX393845,DRS407003,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 3,zebrafish larval gut replicate 3,SAMD00529459,,sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529459,DRX393845,AR012 gut 5 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529459,,,,3463982046.0,27491921.0,DRR408239,0:126 1:0,A:842552557;C:849757648;G:837664725;T:933942026;N:65090,126,0,,,842552557,849757648,837664725,933942026,65090,DRX393845,DRS407003,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
36,DRR408238,DRX393844,DRS407002,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 2,zebrafish larval gut replicate 2,SAMD00529458,,sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529458,DRX393844,AR005 gut 3 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529458,,,,3782320416.0,30018416.0,DRR408238,0:126 1:0,A:930337206;C:920645770;G:906559955;T:1024704277;N:73208,126,0,,,930337206,920645770,906559955,1024704277,73208,DRX393844,DRS407002,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
37,DRR408237,DRX393843,DRS407001,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 1,zebrafish larval gut replicate 1,SAMD00529457,,sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529457,DRX393843,AR002 gut 1 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529457,,,,3606885828.0,28626078.0,DRR408237,0:126 1:0,A:879148446;C:885673723;G:870330963;T:971663212;N:69484,126,0,,,879148446,885673723,870330963,971663212,69484,DRX393843,DRS407001,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
38,DRR408248,DRX393854,DRS407179,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3,zebrafish ENCDC replicate 3,SAMD00529468,,sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529468,DRX393854,190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529468,,,,3803721121.0,24526633.0,DRR408248,0:77.54 1:77.54,A:999106107;C:897663781;G:921501114;T:979486853;N:5963266,77,77,,,999106107,897663781,921501114,979486853,5963266,DRX393854,DRS407179,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
39,DRR408247,DRX393853,DRS407178,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2,zebrafish ENCDC replicate 2,SAMD00529467,,sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529467,DRX393853,190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529467,,,,3436798274.0,22156202.0,DRR408247,0:77.56 1:77.56,A:900848174;C:812031426;G:832960423;T:885671203;N:5287048,77,77,,,900848174,812031426,832960423,885671203,5287048,DRX393853,DRS407178,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
40,DRR408246,DRX393852,DRS407177,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1,zebrafish ENCDC replicate 1,SAMD00529466,,sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529466,DRX393852,190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529466,,,,3582073512.0,23135170.0,DRR408246,0:77.41 1:77.42,A:943152815;C:841972211;G:863627245;T:927361159;N:5960082,77,77,,,943152815,841972211,863627245,927361159,5960082,DRX393852,DRS407177,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
41,DRR408245,DRX393851,DRS407176,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 3,zebrafish EN replicate 3,SAMD00529465,,sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529465,DRX393851,190326ENvsNC N703 5day;EntericNeuron;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529465,,,,3729799291.0,23985772.0,DRR408245,0:77.75 1:77.75,A:978752781;C:879988139;G:903976580;T:962122970;N:4958821,77,77,,,978752781,879988139,903976580,962122970,4958821,DRX393851,DRS407176,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
42,DRR408244,DRX393850,DRS407175,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 2,zebrafish EN replicate 2,SAMD00529464,,sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529464,DRX393850,190326ENvsNC N702 5day;EntericNeuron;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529464,,,,3315994810.0,21477755.0,DRR408244,0:77.19 1:77.20,A:873970427;C:778042505;G:798459853;T:859611841;N:5910184,77,77,,,873970427,778042505,798459853,859611841,5910184,DRX393850,DRS407175,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
43,DRR408243,DRX393849,DRS407174,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 1,zebrafish EN replicate 1,SAMD00529463,,sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529463,DRX393849,190326ENvsNC N701 5day;EntericNeuron;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529463,,,,2999501518.0,19455440.0,DRR408243,0:77.08 1:77.09,A:788053541;C:705895776;G:724185148;T:775760738;N:5606315,77,77,,,788053541,705895776,724185148,775760738,5606315,DRX393849,DRS407174,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
9331,ERR2862354,ERX2868592,ERS2866329,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUC,SAMEA5055152,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055152|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUC|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUC p,TUC p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,12890102400.0,64450512.0,E MTAB 7349:AGCGATAG AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3347844573;C:3078635366;G:3118813009;T:3343385073;N:1424379,100,100,,,3347844573,3078635366,3118813009,3343385073,1424379,ERX2868592,ERS2866329,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89165,0.8896,0.26768,0.26518,0.75142,0.75459,0.60855,0.6105,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9332,ERR2862353,ERX2868591,ERS2866328,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUB,SAMEA5055151,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055151|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUB|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUB|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUB p,TUB p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz,fastq fastq,15345882200.0,76729411.0,E MTAB 7349:TCTCGCGC AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:4257362303;C:3394893224;G:3451042837;T:4240872487;N:1711349,100,100,,,4257362303,3394893224,3451042837,4240872487,1711349,ERX2868591,ERS2866328,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.86888,0.86735,0.45025,0.44476,0.72036,0.72529,0.56048,0.56274,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9333,ERR2862352,ERX2868590,ERS2866327,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUA,SAMEA5055150,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055150|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUA|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUA|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUA p,TUA p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,11985547000.0,59927735.0,E MTAB 7349:TCCGCGAA AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3239652711;C:2732996991;G:2737809176;T:3273773368;N:1314754,100,100,,,3239652711,2732996991,2737809176,3273773368,1314754,ERX2868590,ERS2866327,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.91524,0.91585,0.32418,0.32053,0.72616,0.72671,0.59362,0.42478,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9334,ERR2862351,ERX2868589,ERS2866326,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,HRASC,SAMEA5055149,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055149|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASC|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:HRASC p,HRASC p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,11297151800.0,56485759.0,E MTAB 7349:CGGCTATG GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3202944476;C:2429970659;G:2461948398;T:3201079699;N:1208568,100,100,,,3202944476,2429970659,2461948398,3201079699,1208568,ERX2868589,ERS2866326,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89842,0.86269,0.32455,0.30708,0.74245,0.75191,0.7454,0.74185,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9335,ERR2862350,ERX2868588,ERS2866325,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,HRASB 1A,SAMEA5055148,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055148|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASB 1A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASB 1A|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:HRASB 1A p,HRASB 1A p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,13035635000.0,65178175.0,E MTAB 7349:TCTCGCGC GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3518767071;C:2991842048;G:3005014068;T:3518541297;N:1470516,100,100,,,3518767071,2991842048,3005014068,3518541297,1470516,ERX2868588,ERS2866325,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89434,0.89384,0.28234,0.28093,0.7274,0.72813,0.6198,0.62424,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9336,ERR2862349,ERX2868587,ERS2866324,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,2A,SAMEA5055147,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055147|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:2A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:2A|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:2A p,2A p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,2000FApplication ReadForward11RApplication ReadReverse101,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz,fastq fastq,11671772800.0,58358864.0,E MTAB 7349:TCCGCGAA GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3164806186;C:2661342106;G:2677258036;T:3167072669;N:1293803,100,100,,,3164806186,2661342106,2677258036,3167072669,1293803,ERX2868587,ERS2866324,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89879,0.89878,0.28162,0.28061,0.73212,0.73452,0.59632,0.60115,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9367,ERR145653,ERX121572,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 B seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_B_1.fq.gz WW3_B_2.fq.gz,fastq fastq,4347695086.0,21523243.0,E MTAB 1155:WW3 B,0:101 1:101,A:1074237454;C:1092333862;G:1102729864;T:1065390007;N:13003899,101,101,,,1074237454,1092333862,1102729864,1065390007,13003899,ERX121572,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95796,0.9583,0.02413,0.02313,0.83946,0.8338,0.51717,0.51633,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9368,ERR145654,ERX121560,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 A seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_A_1.fq.gz WW4_A_2.fq.gz,fastq fastq,80948470.0,400735.0,E MTAB 1155:WW4 A,0:101 1:101,A:21174054;C:19268727;G:19622428;T:20880804;N:2457,101,101,,,21174054,19268727,19622428,20880804,2457,ERX121560,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93674,0.92652,0.0383,0.03971,0.84776,0.86028,0.52028,0.51601,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9369,ERR145639,ERX121583,ERS151247,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW4 F M pooled fish,SAMEA1487357,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487357|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW4 seq,CW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW4_1.fq.gz CW4_2.fq.gz,fastq fastq,7322391324.0,36249462.0,E MTAB 1155:CW4,0:101 1:101,A:1915177797;C:1750141576;G:1768328049;T:1887892000;N:851902,101,101,,,1915177797,1750141576,1768328049,1887892000,851902,ERX121583,ERS151247,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94177,0.93855,0.04669,0.04835,0.81227,0.81663,0.5297,0.53381,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9370,ERR145632,ERX121582,ERS151246,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH2 F M pooled fish,SAMEA1487358,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487358|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH2 seq,CH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH2_1.fq.gz CH2_2.fq.gz,fastq fastq,6008384960.0,29744480.0,E MTAB 1155:CH2,0:101 1:101,A:1551084475;C:1456651824;G:1467972620;T:1531930144;N:745897,101,101,,,1551084475,1456651824,1467972620,1531930144,745897,ERX121582,ERS151246,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94484,0.94325,0.04187,0.04238,0.81448,0.8172,0.46639,0.50253,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9371,ERR145634,ERX121581,ERS151245,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH4 F M pooled fish,SAMEA1487361,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487361|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH4 seq,CH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH4_1.fq.gz CH4_2.fq.gz,fastq fastq,5647385104.0,27957352.0,E MTAB 1155:CH4,0:101 1:101,A:1469982057;C:1356659164;G:1371916498;T:1448143269;N:684116,101,101,,,1469982057,1356659164,1371916498,1448143269,684116,ERX121581,ERS151245,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93865,0.93633,0.0439,0.04446,0.80549,0.80864,0.53045,0.51098,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9372,ERR145651,ERX121579,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 B seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_B_1.fq.gz WW2_B_2.fq.gz,fastq fastq,4738967672.0,23460236.0,E MTAB 1155:WW2 B,0:101 1:101,A:1175576318;C:1183749238;G:1198839519;T:1166587116;N:14215481,101,101,,,1175576318,1183749238,1198839519,1166587116,14215481,ERX121579,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95497,0.95617,0.02438,0.0233,0.82909,0.82455,0.51164,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9373,ERR145652,ERX121578,ERS151242,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW3 F M pooled fish,SAMEA1487368,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW3 A seq,WW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW3_A_1.fq.gz WW3_A_2.fq.gz,fastq fastq,229808532.0,1137666.0,E MTAB 1155:WW3 A,0:101 1:101,A:59360822;C:55502890;G:56337453;T:58600433;N:6934,101,101,,,59360822,55502890,56337453,58600433,6934,ERX121578,ERS151242,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93623,0.92715,0.03151,0.03268,0.83735,0.84952,0.52265,0.5038,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9374,ERR145649,ERX121577,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 B seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_B_1.fq.gz WW1_B_2.fq.gz,fastq fastq,7635373356.0,37798878.0,E MTAB 1155:WW1 B,0:101 1:101,A:1902965653;C:1900547622;G:1920575326;T:1888470954;N:22813801,101,101,,,1902965653,1900547622,1920575326,1888470954,22813801,ERX121577,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95977,0.95988,0.02636,0.02563,0.84279,0.83808,0.52131,0.45646,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9375,ERR145636,ERX121576,ERS151244,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW2 F M pooled fish,SAMEA1487364,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487364|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW2 seq,CW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW2_1.fq.gz CW2_2.fq.gz,fastq fastq,7748012798.0,38356499.0,E MTAB 1155:CW2,0:101 1:101,A:2015650126;C:1864022271;G:1874527501;T:1992894699;N:918201,101,101,,,2015650126,1864022271,1874527501,1992894699,918201,ERX121576,ERS151244,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94537,0.94243,0.04249,0.04301,0.82213,0.82552,0.52811,0.53747,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9376,ERR145646,ERX121571,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 A seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_A_1.fq.gz WH4_A_2.fq.gz,fastq fastq,812883148.0,4024174.0,E MTAB 1155:WH4 A,0:101 1:101,A:209997189;C:196285019;G:198925947;T:207278009;N:396984,101,101,,,209997189,196285019,198925947,207278009,396984,ERX121571,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94663,0.91942,0.03602,0.03591,0.8424,0.85462,0.51702,0.51147,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9377,ERR145647,ERX121570,ERS151241,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH4 F M pooled fish,SAMEA1487367,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH4 B seq,WH4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH4_B_1.fq.gz WH4_B_2.fq.gz,fastq fastq,10768144694.0,53307647.0,E MTAB 1155:WH4 B,0:101 1:101,A:2682817583;C:2706807352;G:2714533015;T:2652309644;N:11677100,101,101,,,2682817583,2706807352,2714533015,2652309644,11677100,ERX121570,ERS151241,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.95867,0.96056,0.02378,0.02413,0.83609,0.83889,0.43331,0.44066,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9378,ERR145655,ERX121569,ERS151233,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW4 F M pooled fish,SAMEA1487359,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW4 B seq,WW4 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW4_B_1.fq.gz WW4_B_2.fq.gz,fastq fastq,6455936968.0,31960084.0,E MTAB 1155:WW4 B,0:101 1:101,A:1610738878;C:1605252294;G:1623372987;T:1597311219;N:19261590,101,101,,,1610738878,1605252294,1623372987,1597311219,19261590,ERX121569,ERS151233,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.96085,0.96101,0.02863,0.02731,0.84995,0.8452,0.52157,0.51189,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9379,ERR145633,ERX121568,ERS151240,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH3 F M pooled fish,SAMEA1487363,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487363|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH3 seq,CH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH3_1.fq.gz CH3_2.fq.gz,fastq fastq,6146419640.0,30427820.0,E MTAB 1155:CH3,0:101 1:101,A:1596666196;C:1479913350;G:1493612614;T:1575480940;N:746540,101,101,,,1596666196,1479913350,1493612614,1575480940,746540,ERX121568,ERS151240,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93901,0.93723,0.04362,0.04417,0.79715,0.7977,0.51473,0.52412,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9380,ERR145650,ERX121567,ERS151239,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW2 F M pooled fish,SAMEA1487360,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW2 A seq,WW2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW2_A_1.fq.gz WW2_A_2.fq.gz,fastq fastq,280038054.0,1386327.0,E MTAB 1155:WW2 A,0:101 1:101,A:72831492;C:67021049;G:68232991;T:71942949;N:9573,101,101,,,72831492,67021049,68232991,71942949,9573,ERX121567,ERS151239,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93032,0.9187,0.03207,0.03356,0.82852,0.84139,0.52376,0.52436,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9381,ERR145637,ERX121565,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 A seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_A_1.fq.gz CW3_A_2.fq.gz,fastq fastq,2104292580.0,10417290.0,E MTAB 1155:CW3 A,0:101 1:101,A:547829220;C:504948167;G:510803037;T:540521191;N:190965,101,101,,,547829220,504948167,510803037,540521191,190965,ERX121565,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93423,0.92981,0.04776,0.04835,0.81245,0.81471,0.51349,0.4822,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9382,ERR145631,ERX121564,ERS151237,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CH1 F M pooled fish,SAMEA1487356,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487356|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CH1 seq,CH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CH1_1.fq.gz CH1_2.fq.gz,fastq fastq,7734471526.0,38289463.0,E MTAB 1155:CH1,0:101 1:101,A:1980474194;C:1892305985;G:1907192207;T:1953595996;N:903144,101,101,,,1980474194,1892305985,1907192207,1953595996,903144,ERX121564,ERS151237,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94403,0.94213,0.03862,0.03913,0.82309,0.82556,0.49626,0.49773,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9383,ERR145635,ERX121562,ERS151235,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW1 F M pooled fish,SAMEA1487366,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487366|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW1 seq,CW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW1_1.fq.gz CW1_2.fq.gz,fastq fastq,6202716838.0,30706519.0,E MTAB 1155:CW1,0:101 1:101,A:1612950873;C:1492406749;G:1504306823;T:1592361004;N:691389,101,101,,,1612950873,1492406749,1504306823,1592361004,691389,ERX121562,ERS151235,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94448,0.94226,0.04304,0.04379,0.81296,0.81489,0.5237,0.52588,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9384,ERR145648,ERX121561,ERS151234,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WW1 F M pooled fish,SAMEA1487370,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WW1 A seq,WW1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WW1_A_1.fq.gz WW1_A_2.fq.gz,fastq fastq,330954174.0,1638387.0,E MTAB 1155:WW1 A,0:101 1:101,A:86485807;C:78916128;G:80103844;T:85437370;N:11025,101,101,,,86485807,78916128,80103844,85437370,11025,ERX121561,ERS151234,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.93321,0.92294,0.03445,0.03581,0.84133,0.85267,0.54253,0.53593,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9385,ERR145638,ERX121559,ERS151232,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,CW3 F M pooled fish,SAMEA1487355,Genepool,AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:CW3 B seq,CW3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,CW3_B_1.fq.gz CW3_B_2.fq.gz,fastq fastq,6504819756.0,32202078.0,E MTAB 1155:CW3 B,0:101 1:101,A:1653674963;C:1600212014;G:1606437826;T:1637400265;N:7094688,101,101,,,1653674963,1600212014,1606437826,1637400265,7094688,ERX121559,ERS151232,ERA140546,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94253,0.94443,0.03782,0.03856,0.80661,0.80801,0.49414,0.51667,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9386,ERR147028,ERX122956,ERS151238,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH3 F M pooled fish,SAMEA1487362,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH3 seq,WH3 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH3_1.fq.gz WH3_2.fq.gz,fastq fastq,3197103894.0,15827247.0,E MTAB 1155:WH3,0:101 1:101,A:829020337;C:767623553;G:780642278;T:818288216;N:1529510,101,101,,,829020337,767623553,780642278,818288216,1529510,ERX122956,ERS151238,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94791,0.91975,0.03726,0.03735,0.84291,0.85622,0.4972,0.50314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9387,ERR147027,ERX122955,ERS151236,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH2 F M pooled fish,SAMEA1487365,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487365|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH2 seq,WH2 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH2_1.fq.gz WH2_2.fq.gz,fastq fastq,3455989922.0,17108861.0,E MTAB 1155:WH2,0:101 1:101,A:902145358;C:824320050;G:837200815;T:890816825;N:1506874,101,101,,,902145358,824320050,837200815,890816825,1506874,ERX122955,ERS151236,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94863,0.92001,0.04084,0.04066,0.83796,0.85263,0.5275,0.51735,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9388,ERR147026,ERX122954,ERS151243,ERP001552,PRJEB3112,The effects of temperature on gene expression in zebrafish,E-MTAB-1155,Transcriptome Analysis,Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.,,,Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction.,WH1 F M pooled fish,SAMEA1487369,Genepool,AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487369|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex,,,,,,,,,The effects of temperature on gene expression in zebrafish,E MTAB 1155:WH1 seq,WH1 pooled extract,The effects of temperature on gene expression in zebrafish,Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations.,Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020FApplication ReadForward11RApplication ReadReverse102,ERP001552,Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish,ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16,WH1_1.fq.gz WH1_2.fq.gz,fastq fastq,3005524064.0,14878832.0,E MTAB 1155:WH1,0:101 1:101,A:780146739;C:722416478;G:730307409;T:771476282;N:1177156,101,101,,,780146739,722416478,730307409,771476282,1177156,ERX122954,ERS151243,ERA142144,"Genepool|Department of Biology, McMaster University","Genepool|Department of Biology, McMaster University",2,0.94764,0.92072,0.03746,0.03773,0.83416,0.84831,0.42239,0.51505,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2012-08-21,Adult,Adult,Whole Organism,All anatomical structures
9711,ERR3366000,ERX3390288,ERS3506636,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 3,SAMEA5702979,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 3 p,WT 5dpf whole 3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz,fastq fastq,7638506536.0,25293068.0,E MTAB 8029:WT 5dpf whole 3 ,0:151 1:151,A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553,151,151,,,2033085216,1787203019,1834311569,1982924179,982553,ERX3390288,ERS3506636,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92943,0.93349,0.06443,0.06476,0.67008,0.68489,0.45244,0.47512,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9712,ERR3365999,ERX3390287,ERS3506635,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 2,SAMEA5702978,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 2 p,WT 5dpf whole 2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz,fastq fastq,8029356446.0,26587273.0,E MTAB 8029:WT 5dpf whole 2 ,0:151 1:151,A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810,151,151,,,2111720421,1902949602,1956400199,2057162414,1123810,ERX3390287,ERS3506635,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93664,0.9394,0.06211,0.06234,0.67036,0.68416,0.44709,0.4713,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9713,ERR3365998,ERX3390286,ERS3506634,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,WT 5dpf whole 1,SAMEA5702977,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 1 p,WT 5dpf whole 1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz,fastq fastq,7581314682.0,25103691.0,E MTAB 8029:WT 5dpf whole 1 ,0:151 1:151,A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540,151,151,,,2028089715,1768357820,1809746152,1974047455,1073540,ERX3390286,ERS3506634,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92712,0.93122,0.06876,0.06853,0.66464,0.67537,0.46592,0.47176,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9714,ERR3365997,ERX3390285,ERS3506633,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl2,SAMEA5702976,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl2 p,c386C T het 5dpf whl2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz,fastq fastq,7431512716.0,24607658.0,E MTAB 8029:c386C T het 5dpf whl 2 ,0:151 1:151,A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572,151,151,,,1981584337,1740735155,1776201259,1931922393,1069572,ERX3390285,ERS3506633,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92957,0.933,0.0653,0.06445,0.66967,0.6788,0.46228,0.46392,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9715,ERR3365996,ERX3390284,ERS3506632,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c386C T het 5dpf whl1,SAMEA5702975,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl1 p,c386C T het 5dpf whl1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz,fastq fastq,7350140024.0,24338212.0,E MTAB 8029:c386C T het 5dpf whl 1 ,0:151 1:151,A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274,151,151,,,1930881649,1748604586,1790297791,1879354724,1001274,ERX3390284,ERS3506632,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93663,0.9384,0.05835,0.05828,0.66557,0.67588,0.467,0.46407,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9716,ERR3365995,ERX3390283,ERS3506631,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,c.386C T het 5dpf whl3,SAMEA5702974,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c.386C T het 5dpf whl3 p,c.386C T het 5dpf whl3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz,fastq fastq,6059681642.0,20065171.0,E MTAB 8029:c386C T het 5dpf whl 3 ,0:151 1:151,A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092,151,151,,,1604034432,1423963595,1467519505,1563303018,861092,ERX3390283,ERS3506631,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93301,0.9374,0.0658,0.06581,0.66681,0.68503,0.46139,0.47743,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9842,ERR4029259,ERX4030575,ERS4514128,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 4,SAMEA6786449,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786449|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 4 p,Sample 4 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz,fastq fastq,4354809436.0,29071030.0,E MTAB 8958:FB4 S41 R,0:74.90 1:74.90,A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114,74,74,,,1140431810,1005396495,1008528915,1171220102,29232114,ERX4030575,ERS4514128,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91143,0.91076,0.10123,0.09941,0.68235,0.68452,0.48713,0.48998,76,74,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9843,ERR4029258,ERX4030574,ERS4514127,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 3,SAMEA6786448,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786448|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 3 p,Sample 3 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz,fastq fastq,3973860397.0,26559713.0,E MTAB 8958:FB3 S40 R,0:74.80 1:74.82,A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766,74,74,,,1038749031,917944667,920080717,1066160216,30925766,ERX4030574,ERS4514127,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91065,0.90981,0.10133,0.09911,0.68789,0.68945,0.47182,0.49996,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9844,ERR4029257,ERX4030573,ERS4514126,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 2,SAMEA6786447,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786447|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 2 p,Sample 2 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz,fastq fastq,4135184845.0,27517010.0,E MTAB 8958:FB2 S39 R,0:75.15 1:75.13,A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419,75,75,,,1084253902,962303819,961163738,1111949967,15513419,ERX4030573,ERS4514126,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91098,0.91057,0.09468,0.09311,0.68095,0.68282,0.49982,0.50146,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9845,ERR4029256,ERX4030572,ERS4514125,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 1,SAMEA6786446,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786446|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 1 p,Sample 1 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 06 17,FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq,fastq fastq,4651073045.0,31021879.0,E MTAB 8958:FB1 S38 R,0:74.96 1:74.97,A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744,74,74,,,1225305023,1072643957,1069905162,1255950159,27268744,ERX4030572,ERS4514125,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91441,0.91282,0.10095,0.09913,0.686,0.68745,0.49433,0.5047,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9846,ERR4029255,ERX4030571,ERS4514124,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 16,SAMEA6786445,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786445|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 16|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 16|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 16 p,Sample 16 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz,fastq fastq,5961540086.0,39717871.0,E MTAB 8958:FB4 S20 R,0:75.07 1:75.03,A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639,75,75,,,1565483441,1390303898,1372759826,1611361282,21631639,ERX4030571,ERS4514124,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90959,0.90989,0.0925,0.09172,0.68787,0.68929,0.49093,0.49057,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9847,ERR4029254,ERX4030570,ERS4514123,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 15,SAMEA6786444,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786444|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 15|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 15|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 15 p,Sample 15 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz,fastq fastq,6835575760.0,45515064.0,E MTAB 8958:FB3 S19 R,0:75.11 1:75.07,A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710,75,75,,,1802176562,1589590146,1564279107,1858606235,20923710,ERX4030570,ERS4514123,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90945,0.91123,0.09519,0.09378,0.67963,0.67961,0.49246,0.49476,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9848,ERR4029253,ERX4030569,ERS4514122,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 14,SAMEA6786443,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 14 p,Sample 14 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz,fastq fastq,5789923311.0,38517674.0,E MTAB 8958:FB2 S18 R,0:75.18 1:75.14,A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457,75,75,,,1520250885,1354960735,1336204150,1565011084,13496457,ERX4030569,ERS4514122,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91863,0.91917,0.08923,0.08753,0.68848,0.68883,0.5042,0.50799,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9849,ERR4029252,ERX4030568,ERS4514121,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 13,SAMEA6786442,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786442|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 13|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 13|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 13 p,Sample 13 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz,fastq fastq,6951804793.0,46295025.0,E MTAB 8958:FB1 S17 R,0:75.10 1:75.06,A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094,75,75,,,1827618209,1618955946,1595802123,1884739421,24689094,ERX4030568,ERS4514121,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90991,0.90972,0.09297,0.09193,0.68284,0.68392,0.49878,0.5017,74,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9850,ERR4029251,ERX4030567,ERS4514120,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 20,SAMEA6786441,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786441|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 20|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 20|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 20 p,Sample 20 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz,fastq fastq,9629684100.0,64667395.0,E MTAB 8958:FB4 S44 R,0:74.47 1:74.44,A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676,74,74,,,2552333346,2176006333,2180111416,2614191329,107041676,ERX4030567,ERS4514120,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90795,0.90756,0.10044,0.09789,0.6888,0.69256,0.50043,0.4932,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9851,ERR4029250,ERX4030566,ERS4514119,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 19,SAMEA6786440,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786440|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 19|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 19|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 19 p,Sample 19 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz,fastq fastq,11268744444.0,75088756.0,E MTAB 8958:FB3 S43 R,0:75.06 1:75.01,A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891,75,75,,,2983863814,2608268633,2555098938,3072413168,49099891,ERX4030566,ERS4514119,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9107,0.91089,0.09522,0.09428,0.69187,0.69266,0.49302,0.49463,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9852,ERR4029249,ERX4030565,ERS4514118,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 18,SAMEA6786439,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786439|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 18|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 18|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 18 p,Sample 18 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz,fastq fastq,10434072067.0,69530304.0,E MTAB 8958:FB2 S42 R,0:75.06 1:75.01,A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042,75,75,,,2749500618,2426208950,2375421255,2834879202,48062042,ERX4030565,ERS4514118,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9084,0.90779,0.0926,0.0917,0.68809,0.68864,0.49817,0.49902,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9853,ERR4029248,ERX4030564,ERS4514117,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 17,SAMEA6786438,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786438|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 17|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 17|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 17 p,Sample 17 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ; il4/13b / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz,fastq fastq,12125040750.0,80781224.0,E MTAB 8958:FB1 S41 R,0:75.08 1:75.02,A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600,75,75,,,3129480022,2890038396,2819859086,3233228646,52434600,ERX4030564,ERS4514117,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91384,0.91301,0.10967,0.10615,0.69006,0.69041,0.51643,0.51985,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9854,ERR4029247,ERX4030563,ERS4514116,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 8,SAMEA6786437,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786437|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 8|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 8 p,Sample 8 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz,fastq fastq,4223131851.0,28165494.0,E MTAB 8958:FB12 S49 R,0:74.95 1:74.99,A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146,74,74,,,1121514270,962554300,967294488,1146544647,25224146,ERX4030563,ERS4514116,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91639,0.91413,0.10604,0.10326,0.68162,0.68458,0.49921,0.50172,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9855,ERR4029246,ERX4030562,ERS4514115,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 7,SAMEA6786436,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786436|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 7|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 7 p,Sample 7 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz,fastq fastq,4670407305.0,31054128.0,E MTAB 8958:FB11 S48 R,0:75.20 1:75.19,A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954,75,75,,,1234494738,1078360233,1084251975,1258088405,15211954,ERX4030562,ERS4514115,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92228,0.92038,0.09418,0.09222,0.68674,0.68862,0.48948,0.48842,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9856,ERR4029245,ERX4030561,ERS4514114,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 6,SAMEA6786435,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786435|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 6|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 6 p,Sample 6 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz,fastq fastq,3970723047.0,26597167.0,E MTAB 8958:FB10 S47 R,0:74.63 1:74.66,A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680,74,74,,,1037861230,915437247,922979694,1056625196,37819680,ERX4030561,ERS4514114,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92474,0.92246,0.0934,0.0916,0.69106,0.69384,0.49058,0.48154,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9857,ERR4029244,ERX4030560,ERS4514113,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 5,SAMEA6786434,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786434|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 5 p,Sample 5 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz,fastq fastq,4267946165.0,28455064.0,E MTAB 8958:FB9 S46 R,0:75.00 1:74.99,A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111,75,74,,,1108310330,999732020,987857724,1148193980,23852111,ERX4030560,ERS4514113,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9223,0.91737,0.09304,0.09006,0.69063,0.6929,0.48978,0.49675,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9858,ERR4029243,ERX4030559,ERS4514112,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 9,SAMEA6786433,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786433|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 9|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 9 p,Sample 9 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz,fastq fastq,3847723303.0,25764874.0,E MTAB 8958:FB17 S54 R,0:74.65 1:74.69,A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451,74,74,,,1009950686,883047473,885821368,1035313325,33590451,ERX4030559,ERS4514112,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91088,0.90785,0.09899,0.09623,0.68822,0.69055,0.48686,0.49337,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9859,ERR4029242,ERX4030558,ERS4514111,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 12,SAMEA6786432,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786432|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 12|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 12 p,Sample 12 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz,fastq fastq,4534822065.0,30209756.0,E MTAB 8958:FB20 S57 R,0:75.06 1:75.06,A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622,75,75,,,1181838544,1056097162,1066594521,1207484216,22807622,ERX4030558,ERS4514111,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91577,0.91513,0.09598,0.09473,0.68931,0.69132,0.49181,0.49786,74,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9860,ERR4029241,ERX4030557,ERS4514110,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 11,SAMEA6786431,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786431|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 11|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 11|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 11 p,Sample 11 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz,fastq fastq,5070571422.0,33987501.0,E MTAB 8958:FB19 S56 R,0:74.58 1:74.61,A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944,74,74,,,1327496786,1163563377,1162870630,1365191685,51448944,ERX4030557,ERS4514110,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91091,0.91003,0.09944,0.09748,0.68745,0.69016,0.49706,0.49287,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9861,ERR4029240,ERX4030556,ERS4514109,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 10,SAMEA6786430,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786430|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 10|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 10 p,Sample 10 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10 / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz,fastq fastq,4411576023.0,29389076.0,E MTAB 8958:FB18 S55 R,0:75.05 1:75.06,A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829,75,75,,,1153821133,1024593137,1029312154,1181989770,21859829,ERX4030556,ERS4514109,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90933,0.90999,0.09581,0.09404,0.68917,0.69199,0.49527,0.49791,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
10060,ERR4795364,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz,fastq,5410723202.0,71707309.0,E MTAB 9727:Sample 4,0:75.46 1:0,A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666,75,0,,,1330416803,531269504,734031980,2814959249,45666,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.33614,,0.21532,,0.99019,,0.41002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10061,ERR4795365,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz,fastq,5414184547.0,71707309.0,E MTAB 9727:Sample 4 1,0:0 1:75.50,A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967,0,75,,,1582938104,1052565419,1177180395,1600161662,1338967,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.84976,,0.28521,,0.85038,,0.5124,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10062,ERR4795362,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz,fastq,4823193891.0,63965519.0,E MTAB 9727:Sample 3,0:75.40 1:0,A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086,75,0,,,1323978162,446831209,581746343,2470114091,524086,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.36549,,0.19722,,0.95552,,0.4702,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10063,ERR4795363,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz,fastq,4828889391.0,63965519.0,E MTAB 9727:Sample 3 1,0:0 1:75.49,A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756,0,75,,,1434099697,964508763,893584575,1534727600,1968756,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.85811,,0.26231,,0.82731,,0.48618,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10064,ERR4795360,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz,fastq,5598371393.0,74235388.0,E MTAB 9727:Sample 2,0:75.41 1:0,A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655,75,0,,,1526486973,558020193,717587491,2795646081,630655,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.28059,,0.19252,,0.96404,,0.4874,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10065,ERR4795361,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz,fastq,5600151371.0,74235388.0,E MTAB 9727:Sample 2 1,0:0 1:75.44,A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060,0,75,,,1850568176,1035622971,1071138281,1640475883,2346060,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.7679,,0.30371,,0.82651,,0.43401,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10066,ERR4795358,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz,fastq,4996502316.0,66258508.0,E MTAB 9727:Sample 1,0:75.41 1:0,A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936,75,0,,,1330744174,451622042,591151500,2622422664,561936,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.29754,,0.17671,,0.9669,,0.45463,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10067,ERR4795359,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz,fastq,4999908389.0,66258508.0,E MTAB 9727:Sample 1 1,0:0 1:75.46,A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512,0,75,,,1591945117,933968124,986108614,1485824022,2062512,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.81333,,0.2466,,0.83027,,0.51572,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10374,ERR8058375,ERX7625096,ERS10119356,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 3,SAMEA12512752,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 3 p,Morphine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz,fastq fastq,11175776640.0,44348320.0,E MTAB 11346:NG 10331 4M lib138515 4790 6 ,0:126 1:126,A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329,126,126,,,3058552548,2537121022,2531362154,3047376587,1364329,ERX7625096,ERS10119356,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93345,0.93836,0.09826,0.09482,0.69497,0.69968,0.46885,0.46966,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10375,ERR8058374,ERX7625095,ERS10119355,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 2,SAMEA12512751,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 2 p,Morphine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz,fastq fastq,10428424776.0,41382638.0,E MTAB 11346:NG 10331 3M lib138512 4790 5 ,0:126 1:126,A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201,126,126,,,2840226558,2379827926,2389813154,2817428937,1128201,ERX7625095,ERS10119355,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94204,0.9476,0.09827,0.09565,0.7008,0.70483,0.47435,0.47651,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10376,ERR8058373,ERX7625094,ERS10119354,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Morphine 1,SAMEA12512750,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Morphine 1 p,Morphine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz,fastq fastq,13158093312.0,52214656.0,E MTAB 11346:NG 10331 2M lib138509 4790 5 ,0:126 1:126,A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572,126,126,,,3613282182,2969954628,2964948806,3608471124,1436572,ERX7625094,ERS10119354,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93755,0.93735,0.11204,0.10849,0.67838,0.68335,0.45142,0.46509,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10377,ERR8058372,ERX7625093,ERS10119353,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 3,SAMEA12512749,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 3 p,Control 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz,fastq fastq,14106514968.0,55978234.0,E MTAB 11346:NG 10331 4C lib138514 4790 6 ,0:126 1:126,A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393,126,126,,,3862641975,3195634147,3187866318,3858673135,1699393,ERX7625093,ERS10119353,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93657,0.93813,0.09783,0.09438,0.68925,0.69605,0.4741,0.47037,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10378,ERR8058371,ERX7625092,ERS10119352,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 2,SAMEA12512748,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 2 p,Control 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz,fastq fastq,8889952680.0,35277590.0,E MTAB 11346:NG 10331 3C lib138511 4790 5 ,0:126 1:126,A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902,126,126,,,2424658667,2024699093,2023098669,2416527349,968902,ERX7625092,ERS10119352,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94168,0.94149,0.09632,0.09404,0.68996,0.69672,0.46007,0.47123,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10379,ERR8058370,ERX7625091,ERS10119351,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Control 1,SAMEA12512747,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Control 1 p,Control 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz,fastq fastq,12714421356.0,50454053.0,E MTAB 11346:NG 10331 2C lib138508 4790 5 ,0:126 1:126,A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272,126,126,,,3470625985,2894721473,2886656166,3461036460,1381272,ERX7625091,ERS10119351,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93951,0.93975,0.10489,0.10173,0.68134,0.68702,0.45337,0.44545,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10380,ERR8058369,ERX7625090,ERS10119350,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 3,SAMEA12512746,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 3 p,Cocaine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz,fastq fastq,9574359984.0,37993492.0,E MTAB 11346:NG 10331 4CC lib138516 4790 6 ,0:126 1:126,A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518,126,126,,,2623103101,2170327733,2166494677,2613276955,1157518,ERX7625090,ERS10119350,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.9366,0.93856,0.10196,0.09901,0.69018,0.69611,0.46501,0.46917,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10381,ERR8058368,ERX7625089,ERS10119349,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 2,SAMEA12512745,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 2 p,Cocaine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz,fastq fastq,6977861604.0,27689927.0,E MTAB 11346:NG 10331 3CC lib138513 4828 1 ,0:126 1:126,A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359,126,126,,,1938593544,1560242508,1564690065,1913028128,1307359,ERX7625089,ERS10119349,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94226,0.9472,0.10354,0.10202,0.69911,0.69891,0.4749,0.47595,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10382,ERR8058367,ERX7625088,ERS10119348,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 1,SAMEA12512744,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,E MTAB 11346:Cocaine 1 p,Cocaine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz,fastq fastq,13608728532.0,54002891.0,E MTAB 11346:NG 10331 2CC lib138510 4790 5 ,0:126 1:126,A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601,126,126,,,3713185950,3097562409,3088976816,3707538756,1464601,ERX7625088,ERS10119348,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93921,0.94011,0.104,0.10075,0.68043,0.68523,0.44482,0.4591,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10391,ERR8516975,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R,0:51 1:51,A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852,51,51,,,1077092958,949537387,955020348,1099432979,20556852,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.9053,0.9259,0.21658,0.22155,0.69369,0.69179,0.50726,0.50871,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10392,ERR8516976,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R,0:51 1:51,A:972081222;C:890179393;G:888655698;T:998443264;N:18934747,51,51,,,972081222,890179393,888655698,998443264,18934747,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86107,0.87807,0.22063,0.23029,0.70859,0.70561,0.51656,0.51946,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10393,ERR8516977,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R,0:51 1:51,A:728798881;C:962223604;G:958876331;T:735449513;N:17094231,51,51,,,728798881,962223604,958876331,735449513,17094231,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.54616,0.55881,0.13313,0.14036,0.84295,0.84185,0.64193,0.59762,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10394,ERR8516972,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R,0:51 1:51,A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786,51,51,,,837274632,1062368015,1049892288,853310517,19213786,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.5726,0.57788,0.13781,0.14082,0.80616,0.80452,0.61581,0.60389,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10395,ERR8516973,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R,0:51 1:51,A:897813231;C:796012893;G:794839496;T:923696030;N:17221274,51,51,,,897813231,796012893,794839496,923696030,17221274,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.92095,0.94156,0.18892,0.20024,0.6901,0.68905,0.49377,0.50086,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10396,ERR8516974,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R,0:51 1:51,A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248,51,51,,,951912827,1107150666,1086060798,973791571,20785248,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.63792,0.62667,0.18547,0.18671,0.78756,0.78549,0.59274,0.55478,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10397,ERR8516969,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R,0:51 1:51,A:925784769;C:934445856;G:959155668;T:924080408;N:18878983,51,51,,,925784769,934445856,959155668,924080408,18878983,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.59503,0.61112,0.1947,0.20225,0.76512,0.76337,0.54584,0.54345,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10398,ERR8516970,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R,0:51 1:51,A:991755033;C:864808531;G:892202564;T:992188806;N:18881958,51,51,,,991755033,864808531,892202564,992188806,18881958,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86612,0.88689,0.26181,0.2728,0.7094,0.7091,0.53639,0.53906,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10399,ERR8516971,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R,0:51 1:51,A:766707527;C:798667604;G:818782599;T:773280942;N:15938306,51,51,,,766707527,798667604,818782599,773280942,15938306,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.88811,0.92834,0.21869,0.22669,0.72878,0.72604,0.55598,0.57831,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10400,ERR8516966,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R,0:51 1:51,A:774360373;C:720215184;G:719479745;T:796239200;N:15182374,51,51,,,774360373,720215184,719479745,796239200,15182374,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.79643,0.81194,0.25554,0.2603,0.72236,0.72021,0.51775,0.51678,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10401,ERR8516967,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R,0:51 1:51,A:739921027;C:667375549;G:663864111;T:764302396;N:14288091,51,51,,,739921027,667375549,663864111,764302396,14288091,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.90817,0.92909,0.23387,0.24814,0.70088,0.69842,0.51238,0.51267,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System