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31 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation = "Brain"

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experiment.platform 2

experiment.library_source 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 31 ✖

technology 1

experiment.library_strategy 1

experiment.library_selection 1

  • PolyA · 31 ✖

experiment.library_layout 1

  • SINGLE · 31 ✖
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
101 101 DRR189403 DRX179868 DRS200418 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 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 3 SAMD00182246   sample name:CSUS Tel 30 2w memory 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182246 DRX179868 CSUS Tel 30 2w memory 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182246       2791119960.0 77531110.0 DRR189403 0:36 A:685050951;C:641519684;G:664655385;T:799677669;N:216271 36       685050951 641519684 664655385 799677669 216271 DRX179868 DRS200418 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89653   0.1773   0.70725   0.49873   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
102 102 DRR189402 DRX179867 DRS200417 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 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 2 SAMD00182245   sample name:CSUS Tel 30 2w memory 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182245 DRX179867 CSUS Tel 30 2w memory 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182245       1505449224.0 41818034.0 DRR189402 0:36 A:369895057;C:346914787;G:358624651;T:429897489;N:117240 36       369895057 346914787 358624651 429897489 117240 DRX179867 DRS200417 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89514   0.17677   0.7025   0.49571   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
103 103 DRR189401 DRX179866 DRS200416 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 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 1 SAMD00182244   sample name:CSUS Tel 30 2w memory 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182244 DRX179866 CSUS Tel 30 2w memory 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182244       2088507024.0 58014084.0 DRR189401 0:36 A:516255405;C:478036869;G:496415722;T:597637091;N:161937 36       516255405 478036869 496415722 597637091 161937 DRX179866 DRS200416 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89533   0.18553   0.70981   0.49554   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
104 104 DRR189400 DRX179865 DRS200401 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 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 3 SAMD00182243   sample name:CSUS Tel 30 1d memory 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182243 DRX179865 CSUS Tel 30 1d memory 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182243       1340808120.0 37244670.0 DRR189400 0:36 A:330513975;C:306935584;G:320089399;T:383165274;N:103888 36       330513975 306935584 320089399 383165274 103888 DRX179865 DRS200401 DRA008864 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89272   0.19494   0.70335   0.49456   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
105 105 DRR189399 DRX179864 DRS200400 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 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 2 SAMD00182242   sample name:CSUS Tel 30 1d memory 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182242 DRX179864 CSUS Tel 30 1d memory 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182242       1279740096.0 35548336.0 DRR189399 0:36 A:314850837;C:294188093;G:304654881;T:365946483;N:99802 36       314850837 294188093 304654881 365946483 99802 DRX179864 DRS200400 DRA008864 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89485   0.18205   0.70593   0.49333   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
106 106 DRR189398 DRX179863 DRS200399 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 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 1 SAMD00182241   sample name:CSUS Tel 30 1d memory 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182241 DRX179863 CSUS Tel 30 1d memory 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182241       3012353100.0 83676475.0 DRR189398 0:36 A:740795057;C:693120664;G:717419185;T:860784745;N:233449 36       740795057 693120664 717419185 860784745 233449 DRX179863 DRS200399 DRA008864 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89676   0.1791   0.70569   0.49835   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
107 107 DRR189397 DRX179862 DRS200428 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 60 min post exposure to the conditioning tank 3 SAMD00182240   sample name:Cont Tel 60 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182240 DRX179862 Cont Tel 60 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182240       5590147750.0 111802955.0 DRR189397 0:50 A:1365131560;C:1269631295;G:1366791321;T:1588422020;N:171554 50       1365131560 1269631295 1366791321 1588422020 171554 DRX179862 DRS200428 DRA008863 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89334   0.16354   0.7011   0.49383   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
108 108 DRR189396 DRX179861 DRS200427 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 60 min post exposure to the conditioning tank 2 SAMD00182239   sample name:Cont Tel 60 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182239 DRX179861 Cont Tel 60 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182239       6429019650.0 128580393.0 DRR189396 0:50 A:1570141412;C:1457539089;G:1572785681;T:1828358007;N:195461 50       1570141412 1457539089 1572785681 1828358007 195461 DRX179861 DRS200427 DRA008863 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89595   0.16204   0.70743   0.49805   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
109 109 DRR189395 DRX179860 DRS200426 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 60 min post exposure to the conditioning tank 1 SAMD00182238   sample name:Cont Tel 60 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182238 DRX179860 Cont Tel 60 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182238       6644185850.0 132883717.0 DRR189395 0:50 A:1637322491;C:1498943556;G:1616212676;T:1891505597;N:201530 50       1637322491 1498943556 1616212676 1891505597 201530 DRX179860 DRS200426 DRA008863 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89573   0.16421   0.7037   0.49805   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
110 110 DRR189394 DRX179859 DRS200407 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 60 min post light stimulation in the conditioning tank 3 SAMD00182237   sample name:CS Tel 60 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182237 DRX179859 CS Tel 60 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182237       1387078956.0 38529971.0 DRR189394 0:36 A:333990578;C:315361737;G:337599372;T:400057968;N:69301 36       333990578 315361737 337599372 400057968 69301 DRX179859 DRS200407 DRA008862 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.88133   0.18418   0.70747   0.4971   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
111 111 DRR189393 DRX179858 DRS200406 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 60 min post light stimulation in the conditioning tank 2 SAMD00182236   sample name:CS Tel 60 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182236 DRX179858 CS Tel 60 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182236       537029424.0 14917484.0 DRR189393 0:36 A:127421487;C:122494467;G:132164579;T:154921150;N:27741 36       127421487 122494467 132164579 154921150 27741 DRX179858 DRS200406 DRA008862 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.88264   0.17793   0.7083   0.49123   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
112 112 DRR189392 DRX179857 DRS200405 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 60 min post light stimulation in the conditioning tank 1 SAMD00182235   sample name:CS Tel 60 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182235 DRX179857 CS Tel 60 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182235       3163663656.0 87879546.0 DRR189392 0:36 A:766146692;C:714108562;G:771785405;T:911468887;N:154110 36       766146692 714108562 771785405 911468887 154110 DRX179857 DRS200405 DRA008862 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.88114   0.1803   0.7052   0.4917   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
113 113 DRR189391 DRX179856 DRS200404 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 60 min post electrical shock delivery in the conditioning tank 3 SAMD00182234   sample name:US Tel 60 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182234 DRX179856 US Tel 60 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182234       1535884704.0 42663464.0 DRR189391 0:36 A:367444721;C:350978310;G:375524359;T:441859454;N:77860 36       367444721 350978310 375524359 441859454 77860 DRX179856 DRS200404 DRA008861 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.88103   0.1788   0.7082   0.49462   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
114 114 DRR189390 DRX179855 DRS200403 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 60 min post electrical shock delivery in the conditioning tank 2 SAMD00182233   sample name:US Tel 60 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182233 DRX179855 US Tel 60 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182233       737309916.0 20480831.0 DRR189390 0:36 A:176982713;C:168284406;G:179343270;T:212662841;N:36686 36       176982713 168284406 179343270 212662841 36686 DRX179855 DRS200403 DRA008861 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.87995   0.18515   0.70816   0.49393   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
115 115 DRR189389 DRX179854 DRS200402 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 60 min post electrical shock delivery in the conditioning tank 1 SAMD00182232   sample name:US Tel 60 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182232 DRX179854 US Tel 60 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182232       595837404.0 16551039.0 DRR189389 0:36 A:143956004;C:134783754;G:145443580;T:171624939;N:29127 36       143956004 134783754 145443580 171624939 29127 DRX179854 DRS200402 DRA008861 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.87682   0.18328   0.70309   0.49081   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
116 116 DRR189388 DRX179853 DRS200452 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 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 3 SAMD00182231   sample name:CSUS Tel 60 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182231 DRX179853 CSUS Tel 60 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182231       608050044.0 16890279.0 DRR189388 0:36 A:145025778;C:137906052;G:149542672;T:175545338;N:30204 36       145025778 137906052 149542672 175545338 30204 DRX179853 DRS200452 DRA008860 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.87983   0.18602   0.70445   0.49195   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
117 117 DRR189387 DRX179852 DRS200451 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 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 2 SAMD00182230   sample name:CSUS Tel 60 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182230 DRX179852 CSUS Tel 60 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182230       777589452.0 21599707.0 DRR189387 0:36 A:185463269;C:177742981;G:190443063;T:223900096;N:40043 36       185463269 177742981 190443063 223900096 40043 DRX179852 DRS200451 DRA008860 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.88331   0.17918   0.70516   0.48956   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
118 118 DRR189386 DRX179851 DRS200450 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 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 1 SAMD00182229   sample name:CSUS Tel 60 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182229 DRX179851 CSUS Tel 60 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182229       2738622348.0 76072843.0 DRR189386 0:36 A:662989485;C:622023190;G:663013857;T:790459930;N:135886 36       662989485 622023190 663013857 790459930 135886 DRX179851 DRS200450 DRA008860 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.87743   0.19164   0.70025   0.49073   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
119 119 DRR189385 DRX179850 DRS200435 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 EMX3 / adult zebrafish 3 SAMD00182228   sample name:Emx3 Adult Tel 3|genotype:Emx3 / |tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182228 DRX179850 Emx3 / Adult Tel 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182228       1323636552.0 36767682.0 DRR189385 0:36 A:309582925;C:310206951;G:325673647;T:378136039;N:36990 36       309582925 310206951 325673647 378136039 36990 DRX179850 DRS200435 DRA008859 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.8932   0.19244   0.71334   0.50591   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
120 120 DRR189384 DRX179849 DRS200434 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 EMX3 / adult zebrafish 2 SAMD00182227   sample name:Emx3 Adult Tel 2|genotype:Emx3 / |tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182227 DRX179849 Emx3 / Adult Tel 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182227       2994105168.0 83169588.0 DRR189384 0:36 A:709730692;C:691531995;G:727245229;T:865514929;N:82323 36       709730692 691531995 727245229 865514929 82323 DRX179849 DRS200434 DRA008859 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90382   0.1826   0.70197   0.49719   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
121 121 DRR189383 DRX179848 DRS200433 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 EMX3 / adult zebrafish 1 SAMD00182226   sample name:Emx3 Adult Tel 1|genotype:Emx3 / |tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182226 DRX179848 Emx3 / Adult Tel 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182226       1151464896.0 31985136.0 DRR189383 0:36 A:272427216;C:266708394;G:280781178;T:331515997;N:32111 36       272427216 266708394 280781178 331515997 32111 DRX179848 DRS200433 DRA008859 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89942   0.17402   0.70364   0.49438   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
122 122 DRR189382 DRX179847 DRS200421 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 wild type adult zebrafish 3 SAMD00182225   sample name:WT Adult Tel 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182225 DRX179847 WT Adult Tel 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182225       2837488824.0 78819134.0 DRR189382 0:36 A:678395895;C:655098137;G:687520693;T:816395518;N:78581 36       678395895 655098137 687520693 816395518 78581 DRX179847 DRS200421 DRA008858 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89483   0.18623   0.70544   0.49839   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
123 123 DRR189381 DRX179846 DRS200420 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 wild type adult zebrafish 2 SAMD00182224   sample name:WT Adult Tel 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182224 DRX179846 WT Adult Tel 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182224       1456800264.0 40466674.0 DRR189381 0:36 A:345320431;C:336838149;G:356264798;T:418336552;N:40334 36       345320431 336838149 356264798 418336552 40334 DRX179846 DRS200420 DRA008858 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89496   0.18691   0.70802   0.49721   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
124 124 DRR189380 DRX179845 DRS200419 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 wild type adult zebrafish 1 SAMD00182223   sample name:WT Adult Tel 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182223 DRX179845 WT Adult Tel 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182223       2533282452.0 70368957.0 DRR189380 0:36 A:602595083;C:585466052;G:616064286;T:729086926;N:70105 36       602595083 585466052 616064286 729086926 70105 DRX179845 DRS200419 DRA008858 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89412   0.19005   0.70816   0.49843   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Adult Adult Brain Nervous System
35869 35869 SRR33094451 SRX28358126 SRS24687216 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     Wildtype2   Wildtype2   breed:zebrafish|age:4 month|collection date:2024 05 14|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy Wildtype2 Wildtype2 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA SINGLE BGISEQ BGISEQ-500   SRP578075     WT2_S1_L001_I1_001.fastq.gz fastq 15183539264.0 1897942408.0 WT2 S1 L001 I1 001.fastq.gz 0:8 A:5024041949;C:2632487194;G:2782260146;T:4744243552;N:506423 8       5024041949 2632487194 2782260146 4744243552 506423 SRX28358126 SRS24687216 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T   under 1.2% mapping rate bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-18 Adult Adult Brain Nervous System
35870 35870 SRR33094452 SRX28358125 SRS24687217 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     Wildtype1   Wildtype1   breed:zebrafish|age:4 month|collection date:2024 05 13|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy Wildtype1 Wildtype1 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA SINGLE BGISEQ BGISEQ-500   SRP578075     WT1_S1_L001_I1_001.fastq.gz fastq 7991376264.0 998922033.0 WT1 S1 L001 I1 001.fastq.gz 0:8 A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175 8       2573734851 1426474966 1492966198 2498173074 27175 SRX28358125 SRS24687217 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T   under 1.2% mapping rate bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-18 Adult Adult Brain Nervous System
39646 39646 SRR2020638 SRX1030028 SRS938356 SRP058038 PRJNA283169 Danio rerio Raw sequence reads PRJNA283169 Other RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.       EGFP 1 EGFP   breed:AB|dev stage:6dpf|sex:pooled male and female|tissue:neurons|BioSampleModel:Model organism or animal                 Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a EGFP 3 EGFP 3 EGFP negative FAC sorted neurons representing cells from the whole head that are not Hcrt neurons. Biological replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP058038     6_yelin_CTTGTA_L006_R1_001.fastq fastq 203005250.0 4060105.0 EGFP 3 0:50 A:55382833;C:45271153;G:41975627;T:56203763;N:4171874 50       55382833 45271153 41975627 56203763 4171874 SRX1030028 SRS938356 SRA266465 Bar Ilan University|Dr. Lior Appelbaum Bar Ilan University 1 0.66895   0.34237   0.80612   0.54884   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Israel 2015-05-13 Larval Larval Brain Nervous System
39647 39647 SRR2020637 SRX1030025 SRS938358 SRP058038 PRJNA283169 Danio rerio Raw sequence reads PRJNA283169 Other RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.       EGFP+ 2 EGFP+   breed:AB|dev stage:6dpf|sex:pooled male and female|tissue:neurons|BioSampleModel:Model organism or animal                 Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a EGFP+ 3 EGFP+ 3 EGFP FAC sorted cell representing Hcrt neurons. Biological replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP058038   loader:latf load 5_yelin_GGCTAC_L002_R2_001.fastq 5_yelin_GGCTAC_L002_R1_001.fastq fastq fastq 1560921064.0 7727332.0 EGFP+ 3 0:101 1:101 A:457609649;C:326096117;G:333133118;T:425493422;N:18588758 101 101     457609649 326096117 333133118 425493422 18588758 SRX1030025 SRS938358 SRA266465 Bar Ilan University|Dr. Lior Appelbaum Bar Ilan University 2 0.70147 0.67398 0.38233 0.37219 0.76611 0.78459 0.55856 0.56314 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Israel 2015-05-18 Larval Larval Brain Nervous System
39648 39648 SRR2020632 SRX1030012 SRS938358 SRP058038 PRJNA283169 Danio rerio Raw sequence reads PRJNA283169 Other RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.       EGFP+ 2 EGFP+   breed:AB|dev stage:6dpf|sex:pooled male and female|tissue:neurons|BioSampleModel:Model organism or animal                 Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a EGFP+ 2 EGFP+ 2 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP058038     3_yelin_GATCAG_L006_R1_001.fastq fastq 224054800.0 4481096.0 EGFP+ 2 0:50 A:65453830;C:45018543;G:43270590;T:65387888;N:4923949 50       65453830 45018543 43270590 65387888 4923949 SRX1030012 SRS938358 SRA266465 Bar Ilan University|Dr. Lior Appelbaum Bar Ilan University 1 0.69174   0.54164   0.78522   0.52912   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Israel 2016-05-06 Larval Larval Brain Nervous System
39649 39649 SRR2020597 SRX1030009 SRS938356 SRP058038 PRJNA283169 Danio rerio Raw sequence reads PRJNA283169 Other RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.       EGFP 1 EGFP   breed:AB|dev stage:6dpf|sex:pooled male and female|tissue:neurons|BioSampleModel:Model organism or animal                 Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a EGFP 1 1 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP058038     2_yelin_ACTTGA_L006_R1_001.fastq fastq 447487500.0 8949750.0 EGFP 1 0:50 A:125532720;C:96024111;G:89577716;T:126552915;N:9800038 50       125532720 96024111 89577716 126552915 9800038 SRX1030009 SRS938356 SRA266465 Bar Ilan University|Dr. Lior Appelbaum Bar Ilan University 1 0.70983   0.38959   0.79592   0.54277   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Israel 2015-05-14 Larval Larval Brain Nervous System
40710 40710 SRR3420426 SRX1660364 SRS1360332 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG01294 brain   strain:TUAB|age:adult|sex:pooled male and female|tissue:Brain|BioSampleModel:Model organism or animal                 AG01294 brain AG01294 brain 1 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG01294_SEQ0273_R1.fastq.gz fastq 1145056584.0 15066534.0 AG01294 run 1 0:76 A:325357280;C:243794215;G:244221355;T:331630380;N:53354 76       325357280 243794215 244221355 331630380 53354 SRX1660364 SRS1360332 SRA395141 Yale University|Giraldez Lab Yale University 1 0.92515   0.20551   0.69128   0.50216   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Adult Adult 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");;