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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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
5795,ERR1698352,ERX1767860,ERS1417534,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 012 up 058 12,SAMEA4518355,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518355|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 012 up 058 12 s,IonXpressRNA 012 up 058 12 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_012_up_058_12.fastq.gz,fastq,2535299006.0,33956077.0,E MTAB 5173:IonXpressRNA 012 up 058 12,0:74.66,A:719061985;C:581906269;G:579932234;T:654398518;N:0,74,,,,719061985,581906269,579932234,654398518,0,ERX1767860,ERS1417534,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.7343,,0.34119,,0.7359,,0.48406,,66,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5796,ERR1698351,ERX1767859,ERS1417533,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 011 up 058 11,SAMEA4518354,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518354|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 011 up 058 11|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 011 up 058 11|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 011 up 058 11 s,IonXpressRNA 011 up 058 11 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_011_up_058_11.fastq.gz,fastq,3400774471.0,38709756.0,E MTAB 5173:IonXpressRNA 011 up 058 11,0:87.85,A:948991439;C:793389977;G:792539547;T:865853508;N:0,87,,,,948991439,793389977,792539547,865853508,0,ERX1767859,ERS1417533,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.63968,,0.27033,,0.75213,,0.47966,,139,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5797,ERR1698350,ERX1767858,ERS1417532,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 010 up 058 10,SAMEA4518353,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518353|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 010 up 058 10|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 010 up 058 10|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 010 up 058 10 s,IonXpressRNA 010 up 058 10 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_010_up_058_10.fastq.gz,fastq,3502667998.0,39204781.0,E MTAB 5173:IonXpressRNA 010 up 058 10,0:89.34,A:976977303;C:803330255;G:808731995;T:913628445;N:0,89,,,,976977303,803330255,808731995,913628445,0,ERX1767858,ERS1417532,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.65846,,0.2815,,0.74028,,0.47784,,86,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5798,ERR1698349,ERX1767857,ERS1417531,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 009 up 058 9,SAMEA4518352,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518352|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 009 up 058 9|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 009 up 058 9|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 009 up 058 9 s,IonXpressRNA 009 up 058 9 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_009_up_058_9.fastq.gz,fastq,3575088264.0,39745481.0,E MTAB 5173:IonXpressRNA 009 up 058 9,0:89.95,A:1011474126;C:809896078;G:807471974;T:946246086;N:0,89,,,,1011474126,809896078,807471974,946246086,0,ERX1767857,ERS1417531,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.65266,,0.30274,,0.75286,,0.48527,,94,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5799,ERR1698348,ERX1767856,ERS1417530,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 008 up 058 8,SAMEA4518351,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518351|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 008 up 058 8|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 008 up 058 8|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 008 up 058 8 s,IonXpressRNA 008 up 058 8 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_008_up_058_8.fastq.gz,fastq,3259710114.0,38530802.0,E MTAB 5173:IonXpressRNA 008 up 058 8,0:84.60,A:916053004;C:755694888;G:751125332;T:836836890;N:0,84,,,,916053004,755694888,751125332,836836890,0,ERX1767856,ERS1417530,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.70995,,0.31365,,0.74781,,0.48846,,61,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5800,ERR1698347,ERX1767855,ERS1417529,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 007 up 058 7,SAMEA4518350,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518350|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 007 up 058 7|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 007 up 058 7|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 007 up 058 7 s,IonXpressRNA 007 up 058 7 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_007_up_058_7.fastq.gz,fastq,2307842164.0,28984666.0,E MTAB 5173:IonXpressRNA 007 up 058 7,0:79.62,A:634041732;C:548565089;G:545418985;T:579816358;N:0,79,,,,634041732,548565089,545418985,579816358,0,ERX1767855,ERS1417529,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.67542,,0.2817,,0.74168,,0.47224,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5801,ERR1698346,ERX1767854,ERS1417528,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 006 up 058 6,SAMEA4518349,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518349|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 006 up 058 6|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 006 up 058 6|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 006 up 058 6 s,IonXpressRNA 006 up 058 6 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_006_up_058_6.fastq.gz,fastq,2239484857.0,27021234.0,E MTAB 5173:IonXpressRNA 006 up 058 6,0:82.88,A:637326624;C:506830056;G:503508207;T:591819970;N:0,82,,,,637326624,506830056,503508207,591819970,0,ERX1767854,ERS1417528,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.66441,,0.31904,,0.74905,,0.47154,,122,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5802,ERR1698345,ERX1767853,ERS1417527,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 005 up 058 5,SAMEA4518348,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518348|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 005 up 058 5|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 005 up 058 5|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 005 up 058 5 s,IonXpressRNA 005 up 058 5 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_005_up_058_5.fastq.gz,fastq,2920608487.0,39573075.0,E MTAB 5173:IonXpressRNA 005 up 058 5,0:73.80,A:814851327;C:678116994;G:691911192;T:735728974;N:0,73,,,,814851327,678116994,691911192,735728974,0,ERX1767853,ERS1417527,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.60005,,0.25542,,0.76481,,0.4886,,12,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5803,ERR1698344,ERX1767852,ERS1417526,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 004 up 058 4,SAMEA4518347,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518347|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 004 up 058 4|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 004 up 058 4|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 004 up 058 4 s,IonXpressRNA 004 up 058 4 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_004_up_058_4.fastq.gz,fastq,2989727396.0,37953454.0,E MTAB 5173:IonXpressRNA 004 up 058 4,0:78.77,A:802963810;C:722434772;G:742850530;T:721478284;N:0,78,,,,802963810,722434772,742850530,721478284,0,ERX1767852,ERS1417526,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.76402,,0.32503,,0.74241,,0.4815,,128,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5804,ERR1698343,ERX1767851,ERS1417525,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 003 up 058 3,SAMEA4518346,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518346|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 003 up 058 3|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 003 up 058 3|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 003 up 058 3 s,IonXpressRNA 003 up 058 3 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_003_up_058_3.fastq.gz,fastq,4068383115.0,41996847.0,E MTAB 5173:IonXpressRNA 003 up 058 3,0:96.87,A:1133167706;C:944306379;G:948626944;T:1042282086;N:0,96,,,,1133167706,944306379,948626944,1042282086,0,ERX1767851,ERS1417525,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.54804,,0.22334,,0.76353,,0.49163,,93,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5805,ERR1698342,ERX1767850,ERS1417524,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 002 up 058 2,SAMEA4518345,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518345|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 002 up 058 2 s,IonXpressRNA 002 up 058 2 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_002_up_058_2.fastq.gz,fastq,2679963893.0,33552723.0,E MTAB 5173:IonXpressRNA 002 up 058 2,0:79.87,A:709092431;C:635329399;G:670478210;T:665063853;N:0,79,,,,709092431,635329399,670478210,665063853,0,ERX1767850,ERS1417524,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.43283,,0.18649,,0.81178,,0.52885,,116,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5806,ERR1698341,ERX1767849,ERS1417523,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 001 up 058 1,SAMEA4518344,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518344|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 001 up 058 1|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 001 up 058 1|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 001 up 058 1 s,IonXpressRNA 001 up 058 1 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_001_up_058_1.fastq.gz,fastq,3358902499.0,39857024.0,E MTAB 5173:IonXpressRNA 001 up 058 1,0:84.27,A:933405205;C:784111716;G:780404241;T:860981337;N:0,84,,,,933405205,784111716,780404241,860981337,0,ERX1767849,ERS1417523,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.71789,,0.33159,,0.76619,,0.514,,56,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
8088,ERR034127,ERX012653,ERS032268,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 50% epiboly stage,zebrafish embryo 50 epiboly,SAMEA791629,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 50epiboly,JKE Drerio rna seq,Transcriptome profiling of 50% epiboly stages of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos                     per developmental stage using Trireagent                     Sigma Aldrich. The total RNA was then processed                     further according to the Small RNA Expression Kit                     Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz,SOLiD_native SOLiD_native,3929903550.0,78598071.0,KI BN JKE DRERIO RNASEQ 2011 50epiboly,0:50,,50,,,,,,,,,ERX012653,ERS032268,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.60757,,0.09893,,0.94899,,0.77821,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
8089,ERR034126,ERX012652,ERS032267,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 512 cell stage,zebrafish embryo 512 cell,SAMEA791632,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 512cell,JKE Drerio rna seq,Transcriptome profiling of 512 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos                     per developmental stage using Trireagent                     Sigma Aldrich. The total RNA was then processed                     further according to the Small RNA Expression Kit                     Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz,SOLiD_native SOLiD_native,3918756250.0,78375125.0,KI BN JKE DRERIO RNASEQ 2011 512cell,0:50,,50,,,,,,,,,ERX012652,ERS032267,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.63824,,0.09111,,0.91969,,0.73496,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Blastula,Embryo,Embryo Imprecise,All anatomical structures
8090,ERR034125,ERX012651,ERS032266,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 16 cell stage,zebrafish embryo 16 cell,SAMEA791631,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 16cell,JKE Drerio rna seq,Transcriptome profiling of 16 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos                     per developmental stage using Trireagent                     Sigma Aldrich. The total RNA was then processed                     further according to the Small RNA Expression Kit                     Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz,SOLiD_native SOLiD_native,4256756500.0,85135130.0,KI BN JKE DRERIO RNASEQ 2011 16cell,0:50,,50,,,,,,,,,ERX012651,ERS032266,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.57946,,0.08115,,0.91896,,0.72164,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
8091,ERR034124,ERX012650,ERS032265,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 1 cell stage,zebrafish embryo 1 cell,SAMEA791630,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 1cell,JKE Drerio rna seq,Transcriptome profiling of 1 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos                 per developmental stage using Trireagent                 Sigma Aldrich. The total RNA was then processed                 further according to the Small RNA Expression Kit                 Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz,SOLiD_native SOLiD_native,3676380950.0,73527619.0,KI BN JKE DRERIO RNASEQ 2011 1cell,0:50,,50,,,,,,,,,ERX012650,ERS032265,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.64855,,0.08432,,0.9052,,0.74223,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Zygote,Embryo,Embryo Imprecise,All anatomical structures
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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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
10374,ERR8058375,ERX7625096,ERS10119356,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 3,SAMEA12512752,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 3 p,Morphine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz,fastq fastq,11175776640.0,44348320.0,E MTAB 11346:NG 10331 4M lib138515 4790 6 ,0:126 1:126,A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329,126,126,,,3058552548,2537121022,2531362154,3047376587,1364329,ERX7625096,ERS10119356,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93345,0.93836,0.09826,0.09482,0.69497,0.69968,0.46885,0.46966,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10375,ERR8058374,ERX7625095,ERS10119355,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 2,SAMEA12512751,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 2 p,Morphine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz,fastq fastq,10428424776.0,41382638.0,E MTAB 11346:NG 10331 3M lib138512 4790 5 ,0:126 1:126,A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201,126,126,,,2840226558,2379827926,2389813154,2817428937,1128201,ERX7625095,ERS10119355,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94204,0.9476,0.09827,0.09565,0.7008,0.70483,0.47435,0.47651,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10376,ERR8058373,ERX7625094,ERS10119354,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 1,SAMEA12512750,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 1 p,Morphine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz,fastq fastq,13158093312.0,52214656.0,E MTAB 11346:NG 10331 2M lib138509 4790 5 ,0:126 1:126,A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572,126,126,,,3613282182,2969954628,2964948806,3608471124,1436572,ERX7625094,ERS10119354,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93755,0.93735,0.11204,0.10849,0.67838,0.68335,0.45142,0.46509,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10377,ERR8058372,ERX7625093,ERS10119353,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 3,SAMEA12512749,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 3 p,Control 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz,fastq fastq,14106514968.0,55978234.0,E MTAB 11346:NG 10331 4C lib138514 4790 6 ,0:126 1:126,A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393,126,126,,,3862641975,3195634147,3187866318,3858673135,1699393,ERX7625093,ERS10119353,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93657,0.93813,0.09783,0.09438,0.68925,0.69605,0.4741,0.47037,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10378,ERR8058371,ERX7625092,ERS10119352,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 2,SAMEA12512748,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 2 p,Control 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz,fastq fastq,8889952680.0,35277590.0,E MTAB 11346:NG 10331 3C lib138511 4790 5 ,0:126 1:126,A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902,126,126,,,2424658667,2024699093,2023098669,2416527349,968902,ERX7625092,ERS10119352,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94168,0.94149,0.09632,0.09404,0.68996,0.69672,0.46007,0.47123,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10379,ERR8058370,ERX7625091,ERS10119351,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 1,SAMEA12512747,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 1 p,Control 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz,fastq fastq,12714421356.0,50454053.0,E MTAB 11346:NG 10331 2C lib138508 4790 5 ,0:126 1:126,A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272,126,126,,,3470625985,2894721473,2886656166,3461036460,1381272,ERX7625091,ERS10119351,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93951,0.93975,0.10489,0.10173,0.68134,0.68702,0.45337,0.44545,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10380,ERR8058369,ERX7625090,ERS10119350,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 3,SAMEA12512746,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 3 p,Cocaine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz,fastq fastq,9574359984.0,37993492.0,E MTAB 11346:NG 10331 4CC lib138516 4790 6 ,0:126 1:126,A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518,126,126,,,2623103101,2170327733,2166494677,2613276955,1157518,ERX7625090,ERS10119350,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.9366,0.93856,0.10196,0.09901,0.69018,0.69611,0.46501,0.46917,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10381,ERR8058368,ERX7625089,ERS10119349,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 2,SAMEA12512745,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 2 p,Cocaine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz,fastq fastq,6977861604.0,27689927.0,E MTAB 11346:NG 10331 3CC lib138513 4828 1 ,0:126 1:126,A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359,126,126,,,1938593544,1560242508,1564690065,1913028128,1307359,ERX7625089,ERS10119349,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94226,0.9472,0.10354,0.10202,0.69911,0.69891,0.4749,0.47595,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10382,ERR8058367,ERX7625088,ERS10119348,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 1,SAMEA12512744,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 1 p,Cocaine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz,fastq fastq,13608728532.0,54002891.0,E MTAB 11346:NG 10331 2CC lib138510 4790 5 ,0:126 1:126,A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601,126,126,,,3713185950,3097562409,3088976816,3707538756,1464601,ERX7625088,ERS10119348,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93921,0.94011,0.104,0.10075,0.68043,0.68523,0.44482,0.4591,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
11238,ERR10782555,ERX10233132,ERS14439197,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 6,E MTAB 12503:Sample 6,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 6 p,Sample 6 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz,fastq fastq,14809693138.0,49038719.0,E MTAB 12503:20170530.A 6 R,0:151 1:151,A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269,151,151,,,4069749497,3367864217,3430269434,3928390721,13419269,ERX10233132,ERS14439197,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.83945,0.69977,0.27269,0.22488,0.74523,0.77654,0.4899,0.4358,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11239,ERR10782554,ERX10233131,ERS14439196,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 5,E MTAB 12503:Sample 5,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 5 p,Sample 5 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz,fastq fastq,14954968728.0,49519764.0,E MTAB 12503:20170530.A 5 R,0:151 1:151,A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280,151,151,,,4063340262,3440933120,3455723079,3981396987,13575280,ERX10233131,ERS14439196,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.85891,0.86859,0.28842,0.28866,0.7349,0.75051,0.45532,0.49145,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11240,ERR10782553,ERX10233130,ERS14439195,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 2,E MTAB 12503:Sample 2,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 2 p,Sample 2 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz,fastq fastq,16267571562.0,53866131.0,E MTAB 12503:20170530.A 2 R,0:151 1:151,A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668,151,151,,,4395815325,3765428574,3780844712,4310729283,14753668,ERX10233130,ERS14439195,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.86977,0.8727,0.28497,0.28427,0.70763,0.72301,0.47478,0.47986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures