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5,389 rows where experiment.library_selection = "cDNA" and tissue_curation = "Brain"

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technology >10

devstage_curation 8

devstage_curation_coarse 6

experiment.platform 4

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 5,389 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • cDNA · 5,389 ✖
Link 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
131 131 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
132 132 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
133 133 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
134 134 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
135 135 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
136 136 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
137 137 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
138 138 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
139 139 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
140 140 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
141 141 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
142 142 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
143 143 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
144 144 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
145 145 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
146 146 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
147 147 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
148 148 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
149 149 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
150 150 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
151 151 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
152 152 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
153 153 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
154 154 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
155 155 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
156 156 DRR067143 DRX061087 DRS034141 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 2 SAMD00057666   sample name:Zebrafish 251A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057666 DRX061087 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057666       2040373922.0 10100861.0 DRR067143 0:101 1:101 A:577691972;C:445051245;G:472607289;T:544962357;N:61059 101 101     577691972 445051245 472607289 544962357 61059 DRX061087 DRS034141 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.83407 0.83802 0.12612 0.12666 0.73675 0.74079 0.4948 0.49282 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
157 157 DRR067142 DRX061086 DRS034140 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 1 SAMD00057665   sample name:Zebrafish 251A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057665 DRX061086 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057665       2033951534.0 10069067.0 DRR067142 0:101 1:101 A:589558269;C:431084184;G:460501802;T:552746498;N:60781 101 101     589558269 431084184 460501802 552746498 60781 DRX061086 DRS034140 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.8958 0.90339 0.13764 0.1385 0.72563 0.72865 0.49373 0.49916 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
158 158 DRR067141 DRX061085 DRS034139 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 3 SAMD00057664   sample name:Zebrafish aldoca 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 3                 Illumina HiSeq 1500 paired end sequencing of SAMD00057664 DRX061085 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057664       1931908608.0 9563904.0 DRR067141 0:101 1:101 A:558444394;C:409856521;G:429168864;T:534380258;N:58571 101 101     558444394 409856521 429168864 534380258 58571 DRX061085 DRS034139 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.88632 0.89109 0.15695 0.15773 0.75694 0.7599 0.46875 0.49236 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
159 159 DRR067140 DRX061084 DRS034138 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 2 SAMD00057663   sample name:Zebrafish aldoca 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057663 DRX061084 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057663       1851108406.0 9163903.0 DRR067140 0:101 1:101 A:537339104;C:390802782;G:416335529;T:506575762;N:55229 101 101     537339104 390802782 416335529 506575762 55229 DRX061084 DRS034138 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.9055 0.91341 0.1515 0.15333 0.76495 0.76719 0.49219 0.49012 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
160 160 DRR067139 DRX061083 DRS034137 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 1 SAMD00057662   sample name:Zebrafish aldoca 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057662 DRX061083 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057662       2000078962.0 9901381.0 DRR067139 0:101 1:101 A:583169141;C:420603631;G:446949308;T:549297272;N:59610 101 101     583169141 420603631 446949308 549297272 59610 DRX061083 DRS034137 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.9056 0.90932 0.15092 0.15179 0.76173 0.7654 0.49028 0.49604 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
161 161 DRR067138 DRX061082 DRS034136 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 2 SAMD00057661   sample name:Zebrafish 152B 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057661 DRX061082 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057661       1997432156.0 9888278.0 DRR067138 0:101 1:101 A:578466824;C:423038930;G:449779231;T:546086391;N:60780 101 101     578466824 423038930 449779231 546086391 60780 DRX061082 DRS034136 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.90322 0.91109 0.1463 0.14811 0.75452 0.75633 0.48303 0.48557 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
162 162 DRR067137 DRX061081 DRS034135 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 1 SAMD00057660   sample name:Zebrafish 152B 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057660 DRX061081 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057660       1908437218.0 9447709.0 DRR067137 0:101 1:101 A:552150223;C:401993096;G:427236477;T:527000978;N:56444 101 101     552150223 401993096 427236477 527000978 56444 DRX061081 DRS034135 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.90474 0.91043 0.17336 0.17401 0.76108 0.76359 0.483 0.48537 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
163 163 DRR067136 DRX061080 DRS034134 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 3 SAMD00057659   sample name:Zebrafish 28C 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 3                 Illumina HiSeq 1500 paired end sequencing of SAMD00057659 DRX061080 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057659       1982971178.0 9816689.0 DRR067136 0:101 1:101 A:504064758;C:488246993;G:520130333;T:470469799;N:59295 101 101     504064758 488246993 520130333 470469799 59295 DRX061080 DRS034134 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.53386 0.54375 0.06072 0.06189 0.76351 0.76641 0.4872 0.48857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
164 164 DRR067135 DRX061079 DRS034133 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 2 SAMD00057658   sample name:Zebrafish 28C 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057658 DRX061079 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057658       1961048320.0 9708160.0 DRR067135 0:101 1:101 A:557469151;C:424691789;G:455244994;T:523583601;N:58785 101 101     557469151 424691789 455244994 523583601 58785 DRX061079 DRS034133 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.84854 0.8526 0.10311 0.1042 0.75227 0.75499 0.49321 0.49435 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
165 165 DRR067134 DRX061078 DRS034132 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 1 SAMD00057657   sample name:Zebrafish 28C 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057657 DRX061078 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057657       1931802760.0 9563380.0 DRR067134 0:101 1:101 A:546501397;C:422500710;G:452200521;T:510543489;N:56643 101 101     546501397 422500710 452200521 510543489 56643 DRX061078 DRS034132 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.85439 0.85613 0.09867 0.09897 0.76871 0.77082 0.48943 0.48936 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
166 166 DRR067133 DRX061077 DRS034131 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 2 SAMD00057656   sample name:Zebrafish 156A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057656 DRX061077 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057656       2054289096.0 10169748.0 DRR067133 0:101 1:101 A:563764176;C:464768863;G:497506420;T:528187503;N:62134 101 101     563764176 464768863 497506420 528187503 62134 DRX061077 DRS034131 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.69311 0.6968 0.12309 0.12389 0.76428 0.76676 0.48379 0.48227 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
167 167 DRR067132 DRX061076 DRS034130 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 1 SAMD00057655   sample name:Zebrafish 156A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057655 DRX061076 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <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> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057655       2152665722.0 10656761.0 DRR067132 0:101 1:101 A:585252781;C:495382257;G:522677749;T:549287359;N:65576 101 101     585252781 495382257 522677749 549287359 65576 DRX061076 DRS034130 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.67771 0.68253 0.12949 0.1303 0.77216 0.77542 0.4951 0.49452 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
260 260 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
261 261 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
262 262 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
263 263 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
264 264 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
265 265 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
266 266 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
267 267 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
268 268 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
269 269 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
270 270 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
271 271 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
272 272 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
273 273 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
274 274 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
275 275 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
276 276 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
277 277 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
278 278 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
279 279 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;