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
44,DRR668250,DRX648352,DRS458865,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 3,Zebrafish 2wpi 3,SAMD00799623,,sample name:Zebrafish 2wpi 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 25|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799623,DRX648352,RNA seq of spinal cord in zebrafish at 2wpi injured 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799623,,,,14782516800.0,73912584.0,DRR668250,0:100 1:100,A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943,100,100,,,4058090278,3335994894,3323563782,4062467903,2399943,DRX648352,DRS458865,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
45,DRR668249,DRX648351,DRS458864,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 2,Zebrafish 2wpi 2,SAMD00799622,,sample name:Zebrafish 2wpi 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799622,DRX648351,RNA seq of spinal cord in zebrafish at 2wpi injured 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799622,,,,13687641800.0,68438209.0,DRR668249,0:100 1:100,A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902,100,100,,,3759784620,3087398782,3083881581,3754378915,2197902,DRX648351,DRS458864,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
46,DRR668248,DRX648350,DRS458863,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 1,Zebrafish 2wpi 1,SAMD00799621,,sample name:Zebrafish 2wpi 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799621,DRX648350,RNA seq of spinal cord in zebrafish at 2wpi injured 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799621,,,,16376197200.0,81880986.0,DRR668248,0:100 1:100,A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189,100,100,,,4485868844,3700974430,3710833937,4475827800,2692189,DRX648350,DRS458863,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
47,DRR668247,DRX648349,DRS458862,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 3,Zebrafish Control 3,SAMD00799620,,sample name:Zebrafish Control 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799620,DRX648349,RNA seq of spinal cord in zebrafish at 0wpi control 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799620,,,,13377538600.0,66887693.0,DRR668247,0:100 1:100,A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800,100,100,,,3725064764,2973653932,2980883214,3695767890,2168800,DRX648349,DRS458862,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
48,DRR668246,DRX648348,DRS458861,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 2,Zebrafish Control 2,SAMD00799619,,sample name:Zebrafish Control 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799619,DRX648348,RNA seq of spinal cord in zebrafish at 0wpi control 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799619,,,,14971411400.0,74857057.0,DRR668246,0:100 1:100,A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904,100,100,,,4160326445,3329083037,3329123314,4150453700,2424904,DRX648348,DRS458861,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
49,DRR668245,DRX648347,DRS458860,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 1,Zebrafish Control 1,SAMD00799618,,sample name:Zebrafish Control 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2024 05 04|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799618,DRX648347,RNA seq of spinal cord in zebrafish at 0wpi control 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799618,,,,13912523800.0,69562619.0,DRR668245,0:100 1:100,A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776,100,100,,,3888902049,3079617959,3075111814,3866655202,2236776,DRX648347,DRS458860,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
131,DRR189373,DRX179838,DRS200446,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Dissociated cells from telencephalon of wild type adult zebrafish 3,SAMD00182216,,sample name:Cell Tel 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182216,DRX179838,Cell Tel 3,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182216,,,,4142772200.0,20713861.0,DRR189373,0:100 1:100,A:1185533233;C:877739936;G:877025820;T:1202041821;N:431390,100,100,,,1185533233,877739936,877025820,1202041821,431390,DRX179838,DRS200446,DRA008855,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.9018,0.90073,0.24953,0.25062,0.67884,0.67957,0.49957,0.5402,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
132,DRR189372,DRX179837,DRS200445,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Dissociated cells from telencephalon of wild type adult zebrafish 2,SAMD00182215,,sample name:Cell Tel 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182215,DRX179837,Cell Tel 2,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182215,,,,5233184600.0,26165923.0,DRR189372,0:100 1:100,A:1522745973;C:1082449570;G:1076728796;T:1550682585;N:577676,100,100,,,1522745973,1082449570,1076728796,1550682585,577676,DRX179837,DRS200445,DRA008855,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89481,0.89419,0.27137,0.27018,0.67639,0.67671,0.54949,0.55323,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
133,DRR189371,DRX179836,DRS200444,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Dissociated cells from telencephalon of wild type adult zebrafish 1,SAMD00182214,,sample name:Cell Tel 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182214,DRX179836,Cell Tel 1,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182214,,,,4407578800.0,22037894.0,DRR189371,0:100 1:100,A:1270948410;C:923917605;G:922122984;T:1290126238;N:463563,100,100,,,1270948410,923917605,922122984,1290126238,463563,DRX179836,DRS200444,DRA008855,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.90057,0.90117,0.24092,0.24074,0.67598,0.67775,0.53184,0.53433,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
134,DRR189370,DRX179835,DRS200415,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of h62A;UAS:GFP adult zebrafish 5,SAMD00182213,,sample name:h62A GFP Tel 5|genotype:hspGFF62A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182213,DRX179835,h62A GFP Tel 5,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182213,,,,2904332400.0,14521662.0,DRR189370,0:100 1:100,A:821602205;C:620206517;G:623738781;T:838474359;N:310538,100,100,,,821602205,620206517,623738781,838474359,310538,DRX179835,DRS200415,DRA008854,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.91925,0.91942,0.14636,0.14584,0.71127,0.71429,0.62818,0.40804,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
135,DRR189369,DRX179834,DRS200414,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of h62A;UAS:GFP adult zebrafish 4,SAMD00182212,,sample name:h62A GFP Tel 4|genotype:hspGFF62A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182212,DRX179834,h62A GFP Tel 4,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182212,,,,4670374000.0,23351870.0,DRR189369,0:100 1:100,A:1294304230;C:1030286884;G:1032728119;T:1312561064;N:493703,100,100,,,1294304230,1030286884,1032728119,1312561064,493703,DRX179834,DRS200414,DRA008854,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.92587,0.92725,0.12279,0.12312,0.71056,0.71293,0.57854,0.57882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
136,DRR189368,DRX179833,DRS200413,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of h62A;UAS:GFP adult zebrafish 3,SAMD00182211,,sample name:h62A GFP Tel 3|genotype:hspGFF62A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182211,DRX179833,h62A GFP Tel 3,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182211,,,,11487645000.0,57438225.0,DRR189368,0:100 1:100,A:3127119396;C:2611288030;G:2547219656;T:3194997425;N:7020493,100,100,,,3127119396,2611288030,2547219656,3194997425,7020493,DRX179833,DRS200413,DRA008854,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.91389,0.91371,0.11188,0.11336,0.74576,0.74639,0.56209,0.56027,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
137,DRR189367,DRX179832,DRS200412,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of h62A;UAS:GFP adult zebrafish 2,SAMD00182210,,sample name:h62A GFP Tel 2|genotype:hspGFF62A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182210,DRX179832,h62A GFP Tel 2,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182210,,,,13536257200.0,67681286.0,DRR189367,0:100 1:100,A:3723068804;C:3049411151;G:2951685691;T:3803778575;N:8312979,100,100,,,3723068804,3049411151,2951685691,3803778575,8312979,DRX179832,DRS200412,DRA008854,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.9136,0.91493,0.14102,0.14249,0.70534,0.70569,0.58385,0.58171,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
138,DRR189366,DRX179831,DRS200411,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of h62A;UAS:GFP adult zebrafish 1,SAMD00182209,,sample name:h62A GFP Tel 1|genotype:hspGFF62A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182209,DRX179831,h62A GFP Tel 1,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182209,,,,13057029600.0,65285148.0,DRR189366,0:100 1:100,A:3609997372;C:2912841795;G:2821782510;T:3704302917;N:8105006,100,100,,,3609997372,2912841795,2821782510,3704302917,8105006,DRX179831,DRS200411,DRA008854,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.90766,0.90786,0.13813,0.14007,0.73677,0.73777,0.55675,0.55743,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
139,DRR189365,DRX179830,DRS200432,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of SAGFF120A;UAS:GFP adult zebrafish 4,SAMD00182208,,sample name:120A GFP Tel 4|genotype:SAGFF120A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00182208,DRX179830,120A GFP Tel 4,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2000 paired end sequencing of SAMD00182208,,,,4105132200.0,20525661.0,DRR189365,0:100 1:100,A:1171500567;C:874901685;G:872257219;T:1186025546;N:447183,100,100,,,1171500567,874901685,872257219,1186025546,447183,DRX179830,DRS200432,DRA008853,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.91106,0.90924,0.18729,0.18688,0.69406,0.69589,0.51697,0.51253,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
140,DRR189364,DRX179829,DRS200431,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of SAGFF120A;UAS:GFP adult zebrafish 3,SAMD00182207,,sample name:120A GFP Tel 3|genotype:SAGFF120A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182207,DRX179829,120A GFP Tel 3,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182207,,,,5062007400.0,25310037.0,DRR189364,0:100 1:100,A:1425414609;C:1105334563;G:1072448536;T:1458726402;N:83290,100,100,,,1425414609,1105334563,1072448536,1458726402,83290,DRX179829,DRS200431,DRA008853,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89598,0.89539,0.2645,0.2668,0.69591,0.6971,0.49901,0.49932,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
141,DRR189363,DRX179828,DRS200430,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of SAGFF120A;UAS:GFP adult zebrafish 2,SAMD00182206,,sample name:120A GFP Tel 2|genotype:SAGFF120A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182206,DRX179828,120A GFP Tel 2,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182206,,,,4148886200.0,20744431.0,DRR189363,0:100 1:100,A:1121946535;C:959659540;G:901840216;T:1165367793;N:72116,100,100,,,1121946535,959659540,901840216,1165367793,72116,DRX179828,DRS200430,DRA008853,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89808,0.89803,0.14106,0.14229,0.74057,0.74073,0.58127,0.58258,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
142,DRR189362,DRX179827,DRS200429,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form telencephalon of SAGFF120A;UAS:GFP adult zebrafish 1,SAMD00182205,,sample name:120A GFP Tel 1|genotype:SAGFF120A;UAS:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182205,DRX179827,120A GFP Tel 1,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182205,,,,5621230800.0,28106154.0,DRR189362,0:100 1:100,A:1511319423;C:1299516107;G:1236814355;T:1573482053;N:98862,100,100,,,1511319423,1299516107,1236814355,1573482053,98862,DRX179827,DRS200429,DRA008853,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.90171,0.90205,0.11967,0.12059,0.74083,0.74113,0.61779,0.61682,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
143,DRR189361,DRX179826,DRS200425,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form whole brain of HuC:GFP adult zebrafish 4,SAMD00182204,,sample name:HuC GFP WB 4|genotype:HuC:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182204,DRX179826,HuC GFP WB 4,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182204,,,,3641515200.0,18207576.0,DRR189361,0:100 1:100,A:1038686472;C:777269450;G:777179582;T:1047994354;N:385342,100,100,,,1038686472,777269450,777179582,1047994354,385342,DRX179826,DRS200425,DRA008852,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.91246,0.9127,0.18566,0.18547,0.70201,0.7024,0.47049,0.47102,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
144,DRR189360,DRX179825,DRS200424,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form whole brain of HuC:GFP adult zebrafish 3,SAMD00182203,,sample name:HuC GFP WB 3|genotype:HuC:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182203,DRX179825,HuC GFP WB 3,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182203,,,,4692211000.0,23461055.0,DRR189360,0:100 1:100,A:1310884816;C:1036187295;G:997846600;T:1347212024;N:80265,100,100,,,1310884816,1036187295,997846600,1347212024,80265,DRX179825,DRS200424,DRA008852,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89626,0.89739,0.18174,0.18338,0.72443,0.72588,0.4577,0.46684,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
145,DRR189359,DRX179824,DRS200423,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form whole brain of HuC:GFP adult zebrafish 2,SAMD00182202,,sample name:HuC GFP WB 2|genotype:HuC:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182202,DRX179824,HuC GFP WB 2,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182202,,,,7514071000.0,37570355.0,DRR189359,0:100 1:100,A:2098251885;C:1661407212;G:1597423444;T:2156861774;N:126685,100,100,,,2098251885,1661407212,1597423444,2156861774,126685,DRX179824,DRS200423,DRA008852,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89548,0.89691,0.26231,0.26473,0.70358,0.70471,0.4732,0.4753,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
146,DRR189358,DRX179823,DRS200422,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,GFP cells form whole brain of HuC:GFP adult zebrafish 1,SAMD00182201,,sample name:HuC GFP WB 1|genotype:HuC:GFP|tissue:brain,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00182201,DRX179823,HuC GFP WB 1,1,The cDNA was amplified using SMARTer v4. Sequence libraries were produced from cDNA using Nextera XT DNA library kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00182201,,,,5175824800.0,25879124.0,DRR189358,0:100 1:100,A:1424688686;C:1174545239;G:1128653980;T:1447848363;N:88532,100,100,,,1424688686,1174545239,1128653980,1447848363,88532,DRX179823,DRS200422,DRA008852,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.91906,0.91958,0.20879,0.21088,0.74787,0.74876,0.45243,0.45221,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
147,DRR051067,DRX045959,DRS057267,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,These cells are from the same fish as h62A GFP plus Tel,GFP  cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish,SAMD00044994,,sample name:h62A GFP minus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044994,DRX045959,h62A GFP minus Tel,1,cDNA synthesis : clontech SMARTer v3  > Library prep : Illumina Nextera XT DNA Library Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044994,,,,17913873600.0,89569368.0,DRR051067,0:100 1:100,A:5009629866;C:3957379257;G:3797879751;T:5144366288;N:4618438,100,100,,,5009629866,3957379257,3797879751,5144366288,4618438,DRX045959,DRS057267,DRA004277,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89075,0.89087,0.23044,0.23295,0.69493,0.69769,0.5366,0.54852,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2018-01-06,Undetermined,Undetermined,Brain,Nervous System
148,DRR051066,DRX045958,DRS057275,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Collected from 40 adult fish by using FACS,GFP+ cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish,SAMD00044995,,sample name:h62A GFP plus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044995,DRX045958,h62A GFP plus Tel,1,cDNA synthesis : clontech SMARTer v3  > Library prep : Illumina Nextera XT DNA Library Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044995,,,,17421256000.0,87106280.0,DRR051066,0:100 1:100,A:4859368314;C:3846634012;G:3717526030;T:4993260256;N:4467388,100,100,,,4859368314,3846634012,3717526030,4993260256,4467388,DRX045958,DRS057275,DRA004276,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.88127,0.88114,0.22941,0.23155,0.72161,0.72437,0.49284,0.49449,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
149,DRR051065,DRX045957,DRS057272,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Telencephalon from adult zebrafrish  30 min post light and electrical shock association in non trace Two Way Active Avoidance conditioning,CS+US telencephalon 30 min post TWAA,SAMD00044990,,sample name:CS+US Tel 30|tissue type:brain|genotype:WT,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044990,DRX045957,CS+US Tel 30,1,Illumina Truseq RNA Library Prep Kit v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044990,,,,20239329200.0,101196646.0,DRR051065,0:100 1:100,A:5347169722;C:4777492672;G:4750401220;T:5361888239;N:2377347,100,100,,,5347169722,4777492672,4750401220,5361888239,2377347,DRX045957,DRS057272,DRA004275,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.93576,0.93353,0.13979,0.14019,0.70043,0.70203,0.48989,0.49214,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
150,DRR051064,DRX045956,DRS057265,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Telencephalon from adult zebrafrish  30 min post light stimulation in Two Way Active Avoidance coditioning,CS telencephalon 30 min post TWAA,SAMD00044991,,sample name:CS Tel 30|tissue type:brain|genotype:WT,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044991,DRX045956,CS Tel 30,1,Illumina Truseq RNA Library Prep Kit v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044991,,,,29268319600.0,146341598.0,DRR051064,0:100 1:100,A:7777792429;C:6878969107;G:6819275179;T:7788795270;N:3487615,100,100,,,7777792429,6878969107,6819275179,7788795270,3487615,DRX045956,DRS057265,DRA004274,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.93646,0.93664,0.14051,0.14191,0.70199,0.70374,0.49256,0.49684,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
151,DRR051063,DRX045955,DRS057266,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,These cells are from the same fish as 120A GFP plus Tel,GFP  cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish,SAMD00044987,,sample name:120A GFP minus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044987,DRX045955,120A GFP minus Tel,1,cDNA synthesis : clontech SMARTer v2  > Library prep : Illumina TrunSeq DNA Sample Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044987,,,,15411400120.0,76294060.0,DRR051063,0:101 1:101,A:4583085286;C:3082552426;G:3134669086;T:4606055524;N:5037798,101,101,,,4583085286,3082552426,3134669086,4606055524,5037798,DRX045955,DRS057266,DRA004273,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89184,0.8842,0.30246,0.30334,0.69232,0.705,0.52824,0.51492,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Japan,2018-01-06,Undetermined,Undetermined,Brain,Nervous System
152,DRR051062,DRX045954,DRS057271,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Collected from 40 adult fish by using FACS,GFP+ cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish,SAMD00044988,,sample name:120A GFP plus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044988,DRX045954,120A GFP plus Tel,1,cDNA synthesis : clontech SMARTer v2  > Library prep : Illumina TrunSeq DNA Sample Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044988,,,,9916242014.0,49090307.0,DRR051062,0:101 1:101,A:2991626000;C:1935418605;G:1974202781;T:3011783158;N:3211470,101,101,,,2991626000,1935418605,1974202781,3011783158,3211470,DRX045954,DRS057271,DRA004272,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.87779,0.86382,0.2948,0.28993,0.72809,0.74075,0.50317,0.49169,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
153,DRR051061,DRX045953,DRS057274,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Collected from 10 adult fish by using FACS,GFP+ cells from whole brain of SAGFFLF231A;UAS:GFP transgenic zebrafish,SAMD00044989,,sample name:231A GFP plus WB|tissue type:brain|genotype:SAGFFLF231A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044989,DRX045953,231A GFP plus WB,1,cDNA synthesis : clontech SMARTer v2  > Library prep : Illumina TrunSeq DNA Sample Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044989,,,,27230654000.0,136153270.0,DRR051061,0:101 1:99,A:7929214734;C:5506861409;G:5563593280;T:8059057191;N:171927386,101,99,,,7929214734,5506861409,5563593280,8059057191,171927386,DRX045953,DRS057274,DRA004271,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.88462,0.88282,0.26215,0.26067,0.72468,0.73555,0.48369,0.48285,101,99,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
154,DRR051060,DRX045952,DRS057269,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Telencephalon of adult zebrafrish barin,zebrafihsh telencephalon,SAMD00044992,,sample name:Tel|tissue type:brain|genotype:WT,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044992,DRX045952,Tel,1,Illumina Truseq RNA Library Prep Kit v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044992,,,,20006128076.0,99040238.0,DRR051060,0:101 1:101,A:5393556813;C:4623783008;G:4592812230;T:5384415659;N:11560366,101,101,,,5393556813,4623783008,4592812230,5384415659,11560366,DRX045952,DRS057269,DRA004270,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.94215,0.94001,0.16398,0.16585,0.69331,0.69479,0.4872,0.48516,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
155,DRR051059,DRX045951,DRS057270,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,Whole brain of adult zebrafish,zebrafish whole brain,SAMD00044993,,sample name:WB|tissue type:brain|genotype:WT,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044993,DRX045951,WB,1,Illumina Truseq RNA Library Prep Kit v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044993,,,,25283347776.0,125165088.0,DRR051059,0:101 1:101,A:6845696813;C:5810492697;G:5775241119;T:6837142940;N:14774207,101,101,,,6845696813,5810492697,5775241119,6837142940,14774207,DRX045951,DRS057270,DRA004269,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.94203,0.94067,0.15107,0.15158,0.68651,0.6882,0.49596,0.49589,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-01-06,Adult,Adult,Brain,Nervous System
260,DRR162481,DRX153100,DRS083161,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 39 mpf zebrafish replicate5,SAMD00152429,,sample name:b39 5|age:39 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152429,DRX153100,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152429,,,,1252728200.0,6263641.0,DRR162481,0:100 1:100,A:367502128;C:257734618;G:257260262;T:368202459;N:2028733,100,100,,,367502128,257734618,257260262,368202459,2028733,DRX153100,DRS083161,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92142,0.8899,0.17636,0.1685,0.70686,0.7166,0.53271,0.54366,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
261,DRR162480,DRX153099,DRS083160,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 39 mpf zebrafish replicate4,SAMD00152428,,sample name:b39 4|age:39 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152428,DRX153099,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152428,,,,1426772800.0,7133864.0,DRR162480,0:100 1:100,A:408404333;C:303657580;G:303201065;T:408996815;N:2513007,100,100,,,408404333,303657580,303201065,408996815,2513007,DRX153099,DRS083160,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92435,0.89379,0.16127,0.15446,0.69844,0.70554,0.53646,0.533,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
262,DRR162479,DRX153098,DRS083159,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 39 mpf zebrafish replicate3,SAMD00152427,,sample name:b39 3|age:39 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152427,DRX153098,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152427,,,,1197809800.0,5989049.0,DRR162479,0:100 1:100,A:348955835;C:249141949;G:248747996;T:348970452;N:1993568,100,100,,,348955835,249141949,248747996,348970452,1993568,DRX153098,DRS083159,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92402,0.89389,0.1731,0.1668,0.70938,0.72892,0.55061,0.56711,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
263,DRR162478,DRX153097,DRS083158,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 39 mpf zebrafish replicate2,SAMD00152426,,sample name:b39 2|age:39 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152426,DRX153097,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152426,,,,1389632200.0,6948161.0,DRR162478,0:100 1:100,A:397337261;C:295934915;G:295794427;T:398240347;N:2325250,100,100,,,397337261,295934915,295794427,398240347,2325250,DRX153097,DRS083158,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92803,0.89621,0.15624,0.14998,0.69988,0.70985,0.54263,0.53655,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
264,DRR162477,DRX153096,DRS083157,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 39 mpf zebrafish replicate1,SAMD00152425,,sample name:b39 1|age:39 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152425,DRX153096,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152425,,,,1413538400.0,7067692.0,DRR162477,0:100 1:100,A:427890787;C:277522619;G:278488081;T:427755965;N:1880948,100,100,,,427890787,277522619,278488081,427755965,1880948,DRX153096,DRS083157,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90967,0.88004,0.20536,0.19647,0.71384,0.72021,0.55413,0.55769,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
265,DRR162476,DRX153095,DRS083156,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 16 mpf zebrafish replicate5,SAMD00152424,,sample name:b16 5|age:16 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152424,DRX153095,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152424,,,,1256635000.0,6283175.0,DRR162476,0:100 1:100,A:385448452;C:241878013;G:242164401;T:385408510;N:1735624,100,100,,,385448452,241878013,242164401,385408510,1735624,DRX153095,DRS083156,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91032,0.87693,0.19953,0.19064,0.72575,0.73474,0.49199,0.5657,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
266,DRR162475,DRX153094,DRS083155,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 16 mpf zebrafish replicate4,SAMD00152423,,sample name:b16 4|age:16 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152423,DRX153094,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152423,,,,2577820600.0,12889103.0,DRR162475,0:100 1:100,A:783031561;C:503484597;G:503899732;T:784003178;N:3401532,100,100,,,783031561,503484597,503899732,784003178,3401532,DRX153094,DRS083155,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91098,0.87948,0.20945,0.19993,0.71758,0.72543,0.56796,0.56453,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
267,DRR162474,DRX153093,DRS083154,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 16 mpf zebrafish replicate3,SAMD00152422,,sample name:b16 3|age:16 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152422,DRX153093,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152422,,,,1147257600.0,5736288.0,DRR162474,0:100 1:100,A:357829214;C:214920802;G:215124134;T:357870811;N:1512639,100,100,,,357829214,214920802,215124134,357870811,1512639,DRX153093,DRS083154,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90822,0.88184,0.20468,0.19612,0.73992,0.74627,0.58395,0.50711,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
268,DRR162473,DRX153092,DRS083153,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 16 mpf zebrafish replicate2,SAMD00152421,,sample name:b16 2|age:16 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152421,DRX153092,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152421,,,,1399740200.0,6998701.0,DRR162473,0:100 1:100,A:420492615;C:278464854;G:278362101;T:420657546;N:1763084,100,100,,,420492615,278464854,278362101,420657546,1763084,DRX153092,DRS083153,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91795,0.88458,0.19015,0.18122,0.71374,0.72318,0.55157,0.55554,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
269,DRR162472,DRX153091,DRS083152,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 16 mpf zebrafish replicate1,SAMD00152420,,sample name:b16 1|age:16 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152420,DRX153091,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152420,,,,1109512400.0,5547562.0,DRR162472,0:100 1:100,A:336800225;C:217086705;G:217195789;T:336929233;N:1500448,100,100,,,336800225,217086705,217195789,336929233,1500448,DRX153091,DRS083152,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91025,0.87734,0.20046,0.19197,0.71774,0.72482,0.52937,0.56111,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
270,DRR162471,DRX153090,DRS083151,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 7 mpf zebrafish replicate5,SAMD00152419,,sample name:b07 5|age:7 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152419,DRX153090,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152419,,,,1472475400.0,7362377.0,DRR162471,0:100 1:100,A:448100356;C:287211180;G:287652290;T:447581010;N:1930564,100,100,,,448100356,287211180,287652290,447581010,1930564,DRX153090,DRS083151,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90584,0.87079,0.21738,0.2083,0.71415,0.7344,0.5518,0.55812,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
271,DRR162470,DRX153089,DRS083150,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 7 mpf zebrafish replicate4,SAMD00152418,,sample name:b07 4|age:7 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152418,DRX153089,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152418,,,,1173234000.0,5866170.0,DRR162470,0:100 1:100,A:349147253;C:236479543;G:237153294;T:348938811;N:1515099,100,100,,,349147253,236479543,237153294,348938811,1515099,DRX153089,DRS083150,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91933,0.88973,0.18681,0.17878,0.71108,0.71867,0.5448,0.55274,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
272,DRR162469,DRX153088,DRS083149,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 7 mpf zebrafish replicate3,SAMD00152417,,sample name:b07 3|age:7 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152417,DRX153088,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152417,,,,1322055600.0,6610278.0,DRR162469,0:100 1:100,A:387777992;C:270907178;G:273067585;T:387904272;N:2398573,100,100,,,387777992,270907178,273067585,387904272,2398573,DRX153088,DRS083149,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91753,0.88469,0.17775,0.17007,0.70656,0.71685,0.5466,0.54528,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
273,DRR162468,DRX153087,DRS083148,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 7 mpf zebrafish replicate2,SAMD00152416,,sample name:b07 2|age:7 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152416,DRX153087,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152416,,,,1160349000.0,5801745.0,DRR162468,0:100 1:100,A:350211581;C:228387129;G:229679563;T:349919152;N:2151575,100,100,,,350211581,228387129,229679563,349919152,2151575,DRX153087,DRS083148,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91146,0.87717,0.20422,0.19494,0.7083,0.72082,0.55642,0.56386,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
274,DRR162467,DRX153086,DRS083147,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 7 mpf zebrafish replicate1,SAMD00152415,,sample name:b07 1|age:7 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152415,DRX153086,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152415,,,,1162314600.0,5811573.0,DRR162467,0:100 1:100,A:344932586;C:233867698;G:235450342;T:345967852;N:2096122,100,100,,,344932586,233867698,235450342,345967852,2096122,DRX153086,DRS083147,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91102,0.88248,0.1897,0.18307,0.70786,0.71687,0.55008,0.54646,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Brain,Nervous System
275,DRR162466,DRX153085,DRS083146,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 2 mpf zebrafish replicate5,SAMD00152414,,sample name:b02 5|age:2 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,DRX153085,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,,,,1184455800.0,5922279.0,DRR162466,0:100 1:100,A:357035323;C:233685447;G:235595745;T:356085837;N:2053448,100,100,,,357035323,233685447,235595745,356085837,2053448,DRX153085,DRS083146,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90819,0.87146,0.20659,0.19751,0.71246,0.72251,0.52523,0.52531,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
276,DRR162465,DRX153084,DRS083145,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 2 mpf zebrafish replicate4,SAMD00152413,,sample name:b02 4|age:2 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,DRX153084,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,,,,1389141000.0,6945705.0,DRR162465,0:100 1:100,A:423029010;C:270113394;G:270981952;T:422602360;N:2414284,100,100,,,423029010,270113394,270981952,422602360,2414284,DRX153084,DRS083145,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90961,0.87739,0.21147,0.20152,0.71492,0.72563,0.53639,0.53779,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
277,DRR162464,DRX153083,DRS083144,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 2 mpf zebrafish replicate3,SAMD00152412,,sample name:b02 3|age:2 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,DRX153083,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,,,,2322459000.0,11612295.0,DRR162464,0:100 1:100,A:701085106;C:457451297;G:460424165;T:699185460;N:4312972,100,100,,,701085106,457451297,460424165,699185460,4312972,DRX153083,DRS083144,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92479,0.89382,0.16108,0.1547,0.73312,0.74121,0.55089,0.55507,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
278,DRR162463,DRX153082,DRS083143,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 2 mpf zebrafish replicate2,SAMD00152411,,sample name:b02 2|age:2 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,DRX153082,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,,,,1188406400.0,5942032.0,DRR162463,0:100 1:100,A:354575190;C:238508166;G:239587004;T:353623510;N:2112530,100,100,,,354575190,238508166,239587004,353623510,2112530,DRX153082,DRS083143,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90922,0.8787,0.20709,0.2009,0.71614,0.7362,0.52768,0.53049,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
279,DRR162462,DRX153081,DRS083142,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,brain sample from 2 mpf zebrafish replicate1,SAMD00152410,,sample name:b02 1|age:2 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,DRX153081,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,,,,1033492200.0,5167461.0,DRR162462,0:100 1:100,A:310135217;C:205335529;G:207428012;T:308760225;N:1833217,100,100,,,310135217,205335529,207428012,308760225,1833217,DRX153081,DRS083142,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9176,0.8829,0.18651,0.17848,0.72099,0.73119,0.54307,0.54697,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
8064,ERR035545,ERX013540,ERS017861,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult brain,SAMEA782568,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782568|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult brain|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 460:Zebrafish adult brain|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460 part2:5625 1,ZFbrain 2 RNA 1523492,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented  LiCl precipitated  reverse transcribed with random primers  a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.,Experimental Factor: ORGANISM PART:brain,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<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>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16,5625_1.srf,srf,4576566720.0,28603542.0,E MTAB 460 part2:5625 1.srf,0:76 1:8 2:76,A:1227184716;C:942715631;G:951021478;T:1219839320;N:6977239,76,8,76,,1227184716,942715631,951021478,1219839320,6977239,ERX013540,ERS017861,ERA033503,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.86503,0.86182,0.22392,0.22256,0.69664,0.69865,0.51454,0.51606,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Brain,Nervous System
8069,ERR023147,ERX009449,ERS017861,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult brain,SAMEA782568,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782568|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult brain|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 460:Zebrafish adult brain|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:3537 7,RNA from Zebrafish adult brain,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:brain,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,3537_7.srf,srf,3047469128.0,20049139.0,E MTAB 460:3537 7.srf,0:76 1:76,A:951431181;C:561974807;G:565451314;T:964940357;N:3671469,76,76,,,951431181,561974807,565451314,964940357,3671469,ERX009449,ERS017861,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.89672,0.89537,0.31092,0.31152,0.75724,0.7583,0.56639,0.56663,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Brain,Nervous System
8070,ERR023144,ERX009448,ERS017861,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult brain,SAMEA782568,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782568|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult brain|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 460:Zebrafish adult brain|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:3212 6,RNA from Zebrafish adult brain,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:brain,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,3212_6.srf,srf,1970995248.0,12967074.0,E MTAB 460:3212 6.srf,0:76 1:76,A:601407561;C:370471604;G:371296333;T:608476094;N:19343656,76,76,,,601407561,370471604,371296333,608476094,19343656,ERX009448,ERS017861,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.90042,0.89919,0.30246,0.30122,0.75534,0.75349,0.57375,0.56725,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Brain,Nervous System
10170,ERR375749,ERX348126,ERS337052,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168448,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 2#3,7941068,Illumina sequencing of library 7941068  constructed from sample accession ERS337052 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 2.  This submission includes reads tagged with the sequence TTAGGC.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_2#3.cram,cram,11298599000.0,56492995.0,SC RUN 10586 2#3,0:100 1:100,A:3356877540;C:2323057831;G:2299363865;T:3303865798;N:15433966,100,100,,,3356877540,2323057831,2299363865,3303865798,15433966,ERX348126,ERS337052,ERA267455,SC,Wellcome Sanger Institute,2,0.91061,0.90958,0.1659,0.16567,0.68398,0.68645,0.53954,0.54231,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
10171,ERR375748,ERX348125,ERS337051,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168447,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 2#2,7941067,Illumina sequencing of library 7941067  constructed from sample accession ERS337051 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 2.  This submission includes reads tagged with the sequence CGATGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_2#2.cram,cram,10462424000.0,52312120.0,SC RUN 10586 2#2,0:100 1:100,A:3035632557;C:2208885147;G:2197231235;T:3006145790;N:14529271,100,100,,,3035632557,2208885147,2197231235,3006145790,14529271,ERX348125,ERS337051,ERA267455,SC,Wellcome Sanger Institute,2,0.91417,0.91329,0.15428,0.15477,0.66882,0.66896,0.52191,0.51898,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
10172,ERR375747,ERX348124,ERS337050,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168446,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 2#1,7941066,Illumina sequencing of library 7941066  constructed from sample accession ERS337050 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 2.  This submission includes reads tagged with the sequence ATCACG.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_2#1.cram,cram,10377603200.0,51888016.0,SC RUN 10586 2#1,0:100 1:100,A:3021582125;C:2187474575;G:2170525378;T:2983668309;N:14352813,100,100,,,3021582125,2187474575,2170525378,2983668309,14352813,ERX348124,ERS337050,ERA267455,SC,Wellcome Sanger Institute,2,0.90978,0.90815,0.15565,0.15454,0.67322,0.67476,0.52923,0.51842,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
10173,ERR375746,ERX348123,ERS337052,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168448,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 1#3,7941068,Illumina sequencing of library 7941068  constructed from sample accession ERS337052 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 1.  This submission includes reads tagged with the sequence TTAGGC.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_1#3.cram,cram,11455059800.0,57275299.0,SC RUN 10586 1#3,0:100 1:100,A:3406564785;C:2353388363;G:2329218644;T:3351844154;N:14043854,100,100,,,3406564785,2353388363,2329218644,3351844154,14043854,ERX348123,ERS337052,ERA267455,SC,Wellcome Sanger Institute,2,0.91087,0.90879,0.16647,0.16616,0.6832,0.68436,0.54098,0.53604,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
10174,ERR375745,ERX348122,ERS337051,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168447,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 1#2,7941067,Illumina sequencing of library 7941067  constructed from sample accession ERS337051 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 1.  This submission includes reads tagged with the sequence CGATGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_1#2.cram,cram,10636681200.0,53183406.0,SC RUN 10586 1#2,0:100 1:100,A:3088549841;C:2244455059;G:2232424530;T:3058125106;N:13126664,100,100,,,3088549841,2244455059,2232424530,3058125106,13126664,ERX348122,ERS337051,ERA267455,SC,Wellcome Sanger Institute,2,0.9134,0.91251,0.15433,0.154,0.66849,0.66949,0.52089,0.53096,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
10175,ERR375744,ERX348121,ERS337050,ERP003756,PRJEB4464,Zebrafish olfactory transcriptomics,Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742,Transcriptome Analysis,The olfactory gene repertoire is largely species specific  shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree  ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families  iii its biology is well known  iv is a commonly used model organism  and it is suitable for subsequent functional analysis.,,,,,SAMEA2168446,SC,ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 10586 1#1,7941066,Illumina sequencing of library 7941066  constructed from sample accession ERS337050 for study accession ERP003756.  This is part of an Illumina multiplexed sequencing run 10586 1.  This submission includes reads tagged with the sequence ATCACG.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003756,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16,10586_1#1.cram,cram,10534775800.0,52673879.0,SC RUN 10586 1#1,0:100 1:100,A:3069581091;C:2219273001;G:2202030288;T:3030929981;N:12961439,100,100,,,3069581091,2219273001,2202030288,3030929981,12961439,ERX348121,ERS337050,ERA267455,SC,Wellcome Sanger Institute,2,0.91028,0.90986,0.15668,0.15607,0.67456,0.67472,0.52998,0.49845,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-11-25,Undetermined,Undetermined,Brain,Nervous System
19493,ERR14085264,ERX13487656,ERS22622156,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 1 Replicate 3,Day 1 Replicate 3,SAMEA117549392,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009436 Day 1 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009436 Day 1 Replicate 3|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9517,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19137_1dpl3_R1.fastq.gz 19138_1dpl3_R2.fastq.gz,fastq fastq,9165478634.0,30349267.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9517,0:151 1:151,A:2646232308;C:1796801479;G:2124056448;T:2588021406;N:10366993,151,151,,,2646232308,1796801479,2124056448,2588021406,10366993,ERX13487656,ERS22622156,ERA31046063,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19494,ERR14085263,ERX13487655,ERS22622154,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 1 Replicate 2,Day 1 Replicate 2,SAMEA117549391,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009435 Day 1 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009435 Day 1 Replicate 2|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9516,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19135_1dpl2_R1.fastq.gz 19136_1dpl2_R2.fastq.gz,fastq fastq,9442039362.0,31265031.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9516,0:151 1:151,A:2725446078;C:1808614751;G:2223018565;T:2675393466;N:9566502,151,151,,,2725446078,1808614751,2223018565,2675393466,9566502,ERX13487655,ERS22622154,ERA31046062,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19495,ERR14085271,ERX13487663,ERS22622318,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 7 Replicate 3,Day 7 Replicate 3,SAMEA117549418,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009442 Day 7 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009442 Day 7 Replicate 3|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9523,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19149_7dpl5_R1.fastq.gz 19150_7dpl5_R2.fastq.gz,fastq fastq,9932206502.0,32888101.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9523,0:151 1:151,A:2877130874;C:2050638794;G:2165950578;T:2827301936;N:11184320,151,151,,,2877130874,2050638794,2165950578,2827301936,11184320,ERX13487663,ERS22622318,ERA31046070,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19496,ERR14085261,ERX13487653,ERS22622089,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 1 Replicate 1,Day 1 Replicate 1,SAMEA117549390,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009434 Day 1 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009434 Day 1 Replicate 1|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9515,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19133_1dpl1_R1.fastq.gz 19134_1dpl1_R2.fastq.gz,fastq fastq,9389201442.0,31090071.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9515,0:151 1:151,A:2731715362;C:1816017173;G:2148260573;T:2683133097;N:10075237,151,151,,,2731715362,1816017173,2148260573,2683133097,10075237,ERX13487653,ERS22622089,ERA31046060,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19497,ERR14085274,ERX13487666,ERS22622321,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Control Replicate 3,Control Replicate 3,SAMEA117549421,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009445 Control Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009445 Control Replicate 3|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9526,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19155_C7_R1.fastq.gz 19156_C7_R2.fastq.gz,fastq fastq,9909221282.0,32811991.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9526,0:151 1:151,A:2850780132;C:1946613930;G:2307229799;T:2793332914;N:11264507,151,151,,,2850780132,1946613930,2307229799,2793332914,11264507,ERX13487666,ERS22622321,ERA31046073,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19498,ERR14085268,ERX13487660,ERS22622316,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 7 Replicate 1,Day 7 Replicate 1,SAMEA117549416,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009440 Day 7 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009440 Day 7 Replicate 1|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9521,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19145_7dpl1_R1.fastq.gz 19146_7dpl1_R2.fastq.gz,fastq fastq,9208706914.0,30492407.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9521,0:151 1:151,A:2666375656;C:1820213036;G:2101314534;T:2611250093;N:9553595,151,151,,,2666375656,1820213036,2101314534,2611250093,9553595,ERX13487660,ERS22622316,ERA31046067,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19499,ERR14085276,ERX13487668,ERS22622315,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 4 Replicate 3,Day 4 Replicate 3,SAMEA117549415,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009439 Day 4 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009439 Day 4 Replicate 3|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9520,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19143_4dpl4_R1.fastq.gz 19144_4dpl4_R2.fastq.gz,fastq fastq,9313489740.0,30839370.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9520,0:151 1:151,A:2667044089;C:1836529353;G:2193641971;T:2605720804;N:10553523,151,151,,,2667044089,1836529353,2193641971,2605720804,10553523,ERX13487668,ERS22622315,ERA31046075,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19500,ERR14085272,ERX13487664,ERS22622319,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Control Replicate 1,Control Replicate 1,SAMEA117549419,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009443 Control Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009443 Control Replicate 1|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9524,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19151_C5_R1.fastq.gz 19152_C5_R2.fastq.gz,fastq fastq,13295515874.0,44024887.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9524,0:151 1:151,A:3841326329;C:2750684077;G:2915049240;T:3777029141;N:11427087,151,151,,,3841326329,2750684077,2915049240,3777029141,11427087,ERX13487664,ERS22622319,ERA31046071,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19501,ERR14085265,ERX13487657,ERS22622177,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 4 Replicate 1,Day 4 Replicate 1,SAMEA117549413,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009437 Day 4 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009437 Day 4 Replicate 1|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9518,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19139_4dpl2_R1.fastq.gz 19140_4dpl2_R2.fastq.gz,fastq fastq,12509373332.0,41421766.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9518,0:151 1:151,A:3636942004;C:2502487228;G:2790329437;T:3565530654;N:14084009,151,151,,,3636942004,2502487228,2790329437,3565530654,14084009,ERX13487657,ERS22622177,ERA31046064,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19502,ERR14085266,ERX13487658,ERS22622210,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 4 Replicate 2,Day 4 Replicate 2,SAMEA117549414,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009438 Day 4 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009438 Day 4 Replicate 2|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9519,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19141_4dpl3_R1.fastq.gz 19142_4dpl3_R2.fastq.gz,fastq fastq,9691702460.0,32091730.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9519,0:151 1:151,A:2791714294;C:1934967288;G:2210755028;T:2743302083;N:10963767,151,151,,,2791714294,1934967288,2210755028,2743302083,10963767,ERX13487658,ERS22622210,ERA31046065,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19503,ERR14085269,ERX13487661,ERS22622317,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Day 7 Replicate 2,Day 7 Replicate 2,SAMEA117549417,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009441 Day 7 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009441 Day 7 Replicate 2|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9522,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19147_7dpl4_R1.fastq.gz 19148_7dpl4_R2.fastq.gz,fastq fastq,9862024420.0,32655710.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9522,0:151 1:151,A:2841799545;C:2048598598;G:2166200803;T:2794242657;N:11182817,151,151,,,2841799545,2048598598,2166200803,2794242657,11182817,ERX13487661,ERS22622317,ERA31046068,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
19504,ERR14085273,ERX13487665,ERS22622320,ERP167301,PRJEB83711,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,"inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243",Other,Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,,RNA seq Control Replicate 2,Control Replicate 2,SAMEA117549420,"Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology",ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009444 Control Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009444 Control Replicate 2|scientific name:Danio rerio,,,,,,,,,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP167301,Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration,ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19,19153_C6_R1.fastq.gz 19154_C6_R2.fastq.gz,fastq fastq,11398526732.0,37743466.0,RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525,0:151 1:151,A:3315198872;C:2268180334;G:2561003095;T:3244771542;N:9372889,151,151,,,3315198872,2268180334,2561003095,3244771542,9372889,ERX13487665,ERS22622320,ERA31046072,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-19,Undetermined,Undetermined,Brain,Nervous System
26386,SRR25917801,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L01_R1_001.fastq.gz 22-02953_S24_L01_R2_001.fastq.gz,fastq fastq,1889616596.0,9640901.0,GSM7761847 r1,0:98 1:98,A:502776047;C:437946838;G:435110760;T:512766381;N:1016570,98,98,,,502776047,437946838,435110760,512766381,1016570,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9328,0.92722,0.09638,0.09803,0.70285,0.70345,0.50688,0.50192,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26387,SRR25917802,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L02_R1_001.fastq.gz 22-02953_S24_L02_R2_001.fastq.gz,fastq fastq,2862274828.0,14603443.0,GSM7761847 r2,0:98 1:98,A:757126187;C:668245308;G:664888408;T:771615407;N:399518,98,98,,,757126187,668245308,664888408,771615407,399518,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94091,0.93645,0.09729,0.09803,0.70309,0.7041,0.51085,0.50502,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26388,SRR25917803,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L03_R1_001.fastq.gz 22-02953_S24_L03_R2_001.fastq.gz,fastq fastq,2584726676.0,13187381.0,GSM7761847 r3,0:98 1:98,A:684660799;C:601450975;G:598598564;T:699408337;N:608001,98,98,,,684660799,601450975,598598564,699408337,608001,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94069,0.93734,0.09389,0.09545,0.70264,0.70254,0.49261,0.50213,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26389,SRR25917804,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L04_R1_001.fastq.gz 22-02953_S24_L04_R2_001.fastq.gz,fastq fastq,4100821760.0,20922560.0,GSM7761847 r4,0:98 1:98,A:1082079470;C:958686210;G:956517599;T:1103432545;N:105936,98,98,,,1082079470,958686210,956517599,1103432545,105936,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94702,0.94327,0.09591,0.09712,0.70252,0.70402,0.51264,0.51319,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26390,SRR25917805,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L01_R1_001.fastq.gz 22-02952_S23_L01_R2_001.fastq.gz,fastq fastq,1992642428.0,10166543.0,GSM7761846 r1,0:98 1:98,A:531507040;C:460525641;G:457631907;T:541925633;N:1052207,98,98,,,531507040,460525641,457631907,541925633,1052207,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93066,0.92518,0.10299,0.10378,0.7067,0.70735,0.49353,0.49352,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26391,SRR25917806,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L02_R1_001.fastq.gz 22-02952_S23_L02_R2_001.fastq.gz,fastq fastq,2995445852.0,15282887.0,GSM7761846 r2,0:98 1:98,A:793690840;C:697826413;G:694428368;T:809079956;N:420275,98,98,,,793690840,697826413,694428368,809079956,420275,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93866,0.93421,0.10232,0.10415,0.7038,0.70496,0.49446,0.49935,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26392,SRR25917807,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L03_R1_001.fastq.gz 22-02952_S23_L03_R2_001.fastq.gz,fastq fastq,2558248644.0,13052289.0,GSM7761846 r3,0:98 1:98,A:678550810;C:594295508;G:591607450;T:693175940;N:618936,98,98,,,678550810,594295508,591607450,693175940,618936,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93834,0.93526,0.10036,0.10226,0.70443,0.70565,0.49418,0.4945,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26393,SRR25917808,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L04_R1_001.fastq.gz 22-02952_S23_L04_R2_001.fastq.gz,fastq fastq,3963250536.0,20220666.0,GSM7761846 r4,0:98 1:98,A:1045663273;C:926206212;G:924140110;T:1067139742;N:101199,98,98,,,1045663273,926206212,924140110,1067139742,101199,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94449,0.94083,0.10086,0.10197,0.70469,0.70569,0.4991,0.49202,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26394,SRR25917809,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L01_R1_001.fastq.gz 22-02951_S22_L01_R2_001.fastq.gz,fastq fastq,2029687408.0,10355548.0,GSM7761845 r1,0:98 1:98,A:538688097;C:471579919;G:470623522;T:547765689;N:1030181,98,98,,,538688097,471579919,470623522,547765689,1030181,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.92721,0.92969,0.09472,0.09676,0.70423,0.70276,0.49981,0.49898,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26395,SRR25917810,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L02_R1_001.fastq.gz 22-02951_S22_L02_R2_001.fastq.gz,fastq fastq,3072360760.0,15675310.0,GSM7761845 r2,0:98 1:98,A:810685642;C:719109817;G:718137072;T:824036555;N:391674,98,98,,,810685642,719109817,718137072,824036555,391674,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9358,0.93813,0.09385,0.09614,0.70341,0.70303,0.49098,0.49194,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26396,SRR25917811,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L03_R1_001.fastq.gz 22-02951_S22_L03_R2_001.fastq.gz,fastq fastq,2765019432.0,14107242.0,GSM7761845 r3,0:98 1:98,A:730929526;C:644675885;G:644121852;T:744649936;N:642233,98,98,,,730929526,644675885,644121852,744649936,642233,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93375,0.93756,0.0926,0.09517,0.70429,0.70358,0.50064,0.50166,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26397,SRR25917812,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L04_R1_001.fastq.gz 22-02951_S22_L04_R2_001.fastq.gz,fastq fastq,4491524436.0,22915941.0,GSM7761845 r4,0:98 1:98,A:1183373286;C:1051469132;G:1052482979;T:1204083766;N:115273,98,98,,,1183373286,1051469132,1052482979,1204083766,115273,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94091,0.94403,0.09318,0.09521,0.70374,0.70234,0.49577,0.49187,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26398,SRR25917813,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L01_R1_001.fastq.gz 22-02949_S21_L01_R2_001.fastq.gz,fastq fastq,2534565376.0,12931456.0,GSM7761844 r1,0:98 1:98,A:674884849;C:586725099;G:584045434;T:687552587;N:1357407,98,98,,,674884849,586725099,584045434,687552587,1357407,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93278,0.9279,0.10047,0.10166,0.70506,0.70461,0.51365,0.5138,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26399,SRR25917814,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L02_R1_001.fastq.gz 22-02949_S21_L02_R2_001.fastq.gz,fastq fastq,3889732308.0,19845573.0,GSM7761844 r2,0:98 1:98,A:1029905526;C:906662466;G:903535838;T:1049088768;N:539710,98,98,,,1029905526,906662466,903535838,1049088768,539710,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94166,0.93609,0.09893,0.10006,0.70313,0.70439,0.51404,0.50855,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26400,SRR25917815,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L03_R1_001.fastq.gz 22-02949_S21_L03_R2_001.fastq.gz,fastq fastq,3291066380.0,16791155.0,GSM7761844 r3,0:98 1:98,A:872393079;C:764845510;G:762405303;T:890638586;N:783902,98,98,,,872393079,764845510,762405303,890638586,783902,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94062,0.93691,0.09836,0.0996,0.70416,0.70461,0.51782,0.50965,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26401,SRR25917816,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L04_R1_001.fastq.gz 22-02949_S21_L04_R2_001.fastq.gz,fastq fastq,5366313988.0,27379153.0,GSM7761844 r4,0:98 1:98,A:1415961559;C:1253439804;G:1252742067;T:1444033449;N:137109,98,98,,,1415961559,1253439804,1252742067,1444033449,137109,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94568,0.94293,0.09906,0.10054,0.70402,0.7052,0.51461,0.52073,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26402,SRR25917817,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L01_R1_001.fastq.gz 22-02948_S20_L01_R2_001.fastq.gz,fastq fastq,2053905168.0,10479108.0,GSM7761843 r1,0:98 1:98,A:547671134;C:475089537;G:473080534;T:556992811;N:1071152,98,98,,,547671134,475089537,473080534,556992811,1071152,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93522,0.9298,0.10197,0.10238,0.70339,0.70421,0.50454,0.50393,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26403,SRR25917818,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L02_R1_001.fastq.gz 22-02948_S20_L02_R2_001.fastq.gz,fastq fastq,3144952300.0,16045675.0,GSM7761843 r2,0:98 1:98,A:832655138;C:733701092;G:731348360;T:846811030;N:436680,98,98,,,832655138,733701092,731348360,846811030,436680,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94365,0.93984,0.10028,0.10124,0.70398,0.70565,0.50353,0.50505,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26404,SRR25917819,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L03_R1_001.fastq.gz 22-02948_S20_L03_R2_001.fastq.gz,fastq fastq,2460170244.0,12551889.0,GSM7761843 r3,0:98 1:98,A:651706233;C:572474025;G:570982999;T:664399947;N:607040,98,98,,,651706233,572474025,570982999,664399947,607040,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9411,0.93886,0.09891,0.10006,0.70485,0.70362,0.50337,0.50208,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26405,SRR25917820,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L04_R1_001.fastq.gz 22-02948_S20_L04_R2_001.fastq.gz,fastq fastq,3890916344.0,19851614.0,GSM7761843 r4,0:98 1:98,A:1025556861;C:910441322;G:909593603;T:1045230061;N:94497,98,98,,,1025556861,910441322,909593603,1045230061,94497,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94835,0.94517,0.09781,0.09849,0.70274,0.70374,0.5027,0.5008,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26406,SRR25917821,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L01_R1_001.fastq.gz 22-02947_S19_L01_R2_001.fastq.gz,fastq fastq,1696563848.0,8655938.0,GSM7761842 r1,0:98 1:98,A:453186259;C:391677304;G:390304899;T:460508753;N:886633,98,98,,,453186259,391677304,390304899,460508753,886633,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9329,0.92803,0.10284,0.10415,0.70611,0.70664,0.49615,0.49305,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26407,SRR25917822,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L02_R1_001.fastq.gz 22-02947_S19_L02_R2_001.fastq.gz,fastq fastq,2634385040.0,13440740.0,GSM7761842 r2,0:98 1:98,A:699185241;C:613094915;G:611213748;T:710534569;N:356567,98,98,,,699185241,613094915,611213748,710534569,356567,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94184,0.93645,0.10113,0.10207,0.70268,0.70345,0.50894,0.50924,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26408,SRR25917823,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L03_R1_001.fastq.gz 22-02947_S19_L03_R2_001.fastq.gz,fastq fastq,2356722424.0,12024094.0,GSM7761842 r3,0:98 1:98,A:626784832;C:546121522;G:545024526;T:638243477;N:548067,98,98,,,626784832,546121522,545024526,638243477,548067,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94068,0.93749,0.09906,0.10122,0.7039,0.70449,0.50662,0.51119,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26409,SRR25917824,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L04_R1_001.fastq.gz 22-02947_S19_L04_R2_001.fastq.gz,fastq fastq,3824206372.0,19511257.0,GSM7761842 r4,0:98 1:98,A:1013047237;C:890237600;G:890115590;T:1030706585;N:99360,98,98,,,1013047237,890237600,890115590,1030706585,99360,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9463,0.94321,0.10017,0.1014,0.7038,0.70437,0.50533,0.51168,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26410,SRR25917825,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L01_R1_001.fastq.gz 22-02946_S18_L01_R2_001.fastq.gz,fastq fastq,2024888936.0,10331066.0,GSM7761841 r1,0:98 1:98,A:542606378;C:466454644;G:464323282;T:550429046;N:1075586,98,98,,,542606378,466454644,464323282,550429046,1075586,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.933,0.92706,0.10233,0.10303,0.70429,0.70465,0.49443,0.48878,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26411,SRR25917826,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L02_R1_001.fastq.gz 22-02946_S18_L02_R2_001.fastq.gz,fastq fastq,3069224368.0,15659308.0,GSM7761841 r2,0:98 1:98,A:816848746;C:712756904;G:710416167;T:828782508;N:420043,98,98,,,816848746,712756904,710416167,828782508,420043,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94117,0.93483,0.10216,0.10274,0.70467,0.7051,0.50931,0.51613,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26412,SRR25917827,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L03_R1_001.fastq.gz 22-02946_S18_L03_R2_001.fastq.gz,fastq fastq,2612758008.0,13330398.0,GSM7761841 r3,0:98 1:98,A:695834172;C:605270278;G:603512924;T:707518532;N:622102,98,98,,,695834172,605270278,603512924,707518532,622102,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94095,0.93716,0.09929,0.10092,0.70343,0.70396,0.49363,0.50028,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26413,SRR25917828,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L04_R1_001.fastq.gz 22-02946_S18_L04_R2_001.fastq.gz,fastq fastq,4163040196.0,21240001.0,GSM7761841 r4,0:98 1:98,A:1104116525;C:968916166;G:968183447;T:1121718793;N:105265,98,98,,,1104116525,968916166,968183447,1121718793,105265,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94611,0.94219,0.09973,0.10107,0.70303,0.70394,0.51684,0.51536,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System