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920 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Brain"

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experiment.library_selection 9

devstage_curation 7

devstage_curation_coarse 6

experiment.platform 4

experiment.library_strategy 4

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 920 ✖

technology 1

  • unknown · 920 ✖

experiment.library_layout 1

  • SINGLE · 920 ✖
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
5795 5795 ERR1698352 ERX1767860 ERS1417534 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 012 up 058 12 SAMEA4518355 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518355|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 012 up 058 12 s IonXpressRNA 012 up 058 12 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_012_up_058_12.fastq.gz fastq 2535299006.0 33956077.0 E MTAB 5173:IonXpressRNA 012 up 058 12 0:74.66 A:719061985;C:581906269;G:579932234;T:654398518;N:0 74       719061985 581906269 579932234 654398518 0 ERX1767860 ERS1417534 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.7343   0.34119   0.7359   0.48406   66   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5796 5796 ERR1698351 ERX1767859 ERS1417533 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 011 up 058 11 SAMEA4518354 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518354|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 011 up 058 11|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 011 up 058 11|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 011 up 058 11 s IonXpressRNA 011 up 058 11 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_011_up_058_11.fastq.gz fastq 3400774471.0 38709756.0 E MTAB 5173:IonXpressRNA 011 up 058 11 0:87.85 A:948991439;C:793389977;G:792539547;T:865853508;N:0 87       948991439 793389977 792539547 865853508 0 ERX1767859 ERS1417533 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.63968   0.27033   0.75213   0.47966   139   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5797 5797 ERR1698350 ERX1767858 ERS1417532 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 010 up 058 10 SAMEA4518353 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518353|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 010 up 058 10|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 010 up 058 10|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 010 up 058 10 s IonXpressRNA 010 up 058 10 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_010_up_058_10.fastq.gz fastq 3502667998.0 39204781.0 E MTAB 5173:IonXpressRNA 010 up 058 10 0:89.34 A:976977303;C:803330255;G:808731995;T:913628445;N:0 89       976977303 803330255 808731995 913628445 0 ERX1767858 ERS1417532 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.65846   0.2815   0.74028   0.47784   86   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5798 5798 ERR1698349 ERX1767857 ERS1417531 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 009 up 058 9 SAMEA4518352 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518352|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 009 up 058 9|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 009 up 058 9|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 009 up 058 9 s IonXpressRNA 009 up 058 9 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_009_up_058_9.fastq.gz fastq 3575088264.0 39745481.0 E MTAB 5173:IonXpressRNA 009 up 058 9 0:89.95 A:1011474126;C:809896078;G:807471974;T:946246086;N:0 89       1011474126 809896078 807471974 946246086 0 ERX1767857 ERS1417531 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.65266   0.30274   0.75286   0.48527   94   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5799 5799 ERR1698348 ERX1767856 ERS1417530 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 008 up 058 8 SAMEA4518351 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518351|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 008 up 058 8|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 008 up 058 8|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 008 up 058 8 s IonXpressRNA 008 up 058 8 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_008_up_058_8.fastq.gz fastq 3259710114.0 38530802.0 E MTAB 5173:IonXpressRNA 008 up 058 8 0:84.60 A:916053004;C:755694888;G:751125332;T:836836890;N:0 84       916053004 755694888 751125332 836836890 0 ERX1767856 ERS1417530 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.70995   0.31365   0.74781   0.48846   61   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5800 5800 ERR1698347 ERX1767855 ERS1417529 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 007 up 058 7 SAMEA4518350 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518350|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 007 up 058 7|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 007 up 058 7|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 007 up 058 7 s IonXpressRNA 007 up 058 7 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_007_up_058_7.fastq.gz fastq 2307842164.0 28984666.0 E MTAB 5173:IonXpressRNA 007 up 058 7 0:79.62 A:634041732;C:548565089;G:545418985;T:579816358;N:0 79       634041732 548565089 545418985 579816358 0 ERX1767855 ERS1417529 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.67542   0.2817   0.74168   0.47224   37   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5801 5801 ERR1698346 ERX1767854 ERS1417528 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 006 up 058 6 SAMEA4518349 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518349|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 006 up 058 6|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 006 up 058 6|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 006 up 058 6 s IonXpressRNA 006 up 058 6 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_006_up_058_6.fastq.gz fastq 2239484857.0 27021234.0 E MTAB 5173:IonXpressRNA 006 up 058 6 0:82.88 A:637326624;C:506830056;G:503508207;T:591819970;N:0 82       637326624 506830056 503508207 591819970 0 ERX1767854 ERS1417528 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.66441   0.31904   0.74905   0.47154   122   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5802 5802 ERR1698345 ERX1767853 ERS1417527 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 005 up 058 5 SAMEA4518348 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518348|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 005 up 058 5|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 005 up 058 5|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 005 up 058 5 s IonXpressRNA 005 up 058 5 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_005_up_058_5.fastq.gz fastq 2920608487.0 39573075.0 E MTAB 5173:IonXpressRNA 005 up 058 5 0:73.80 A:814851327;C:678116994;G:691911192;T:735728974;N:0 73       814851327 678116994 691911192 735728974 0 ERX1767853 ERS1417527 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.60005   0.25542   0.76481   0.4886   12   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5803 5803 ERR1698344 ERX1767852 ERS1417526 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 004 up 058 4 SAMEA4518347 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518347|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 004 up 058 4|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 004 up 058 4|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 004 up 058 4 s IonXpressRNA 004 up 058 4 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_004_up_058_4.fastq.gz fastq 2989727396.0 37953454.0 E MTAB 5173:IonXpressRNA 004 up 058 4 0:78.77 A:802963810;C:722434772;G:742850530;T:721478284;N:0 78       802963810 722434772 742850530 721478284 0 ERX1767852 ERS1417526 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.76402   0.32503   0.74241   0.4815   128   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5804 5804 ERR1698343 ERX1767851 ERS1417525 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 003 up 058 3 SAMEA4518346 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518346|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 003 up 058 3|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 003 up 058 3|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 003 up 058 3 s IonXpressRNA 003 up 058 3 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_003_up_058_3.fastq.gz fastq 4068383115.0 41996847.0 E MTAB 5173:IonXpressRNA 003 up 058 3 0:96.87 A:1133167706;C:944306379;G:948626944;T:1042282086;N:0 96       1133167706 944306379 948626944 1042282086 0 ERX1767851 ERS1417525 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.54804   0.22334   0.76353   0.49163   93   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5805 5805 ERR1698342 ERX1767850 ERS1417524 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 002 up 058 2 SAMEA4518345 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518345|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 002 up 058 2 s IonXpressRNA 002 up 058 2 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_002_up_058_2.fastq.gz fastq 2679963893.0 33552723.0 E MTAB 5173:IonXpressRNA 002 up 058 2 0:79.87 A:709092431;C:635329399;G:670478210;T:665063853;N:0 79       709092431 635329399 670478210 665063853 0 ERX1767850 ERS1417524 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.43283   0.18649   0.81178   0.52885   116   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
5806 5806 ERR1698341 ERX1767849 ERS1417523 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 001 up 058 1 SAMEA4518344 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518344|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 001 up 058 1|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 001 up 058 1|sex:female                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 001 up 058 1 s IonXpressRNA 001 up 058 1 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: female:sex|Experimental Factor: n1:compound RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16 IonXpressRNA_001_up_058_1.fastq.gz fastq 3358902499.0 39857024.0 E MTAB 5173:IonXpressRNA 001 up 058 1 0:84.27 A:933405205;C:784111716;G:780404241;T:860981337;N:0 84       933405205 784111716 780404241 860981337 0 ERX1767849 ERS1417523 ERA739176 School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive 1 0.71789   0.33159   0.76619   0.514   56   B   usable mapping rate ion_torrent ion_torrent full_length random_priming ribozero bulk unknown unknown   Sweden 2016-10-19 Pharyngula Embryo Brain Nervous System
34964 34964 SRR32588721 SRX27895230 SRS24266233 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F B   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 Iso Seq RNA from brain C2 F2 F B C2 F2 F B The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m64467e_240523_204656.skera.flnc.fastq.gz fastq 11267908778.0 6337509.0 m64467e 240523 204656.skera.flnc.fastq.gz 0:1777.97 A:3374083285;C:2369790412;G:2399920883;T:3124114198;N:0 1777       3374083285 2369790412 2399920883 3124114198 0 SRX27895230 SRS24266233 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Brain Nervous System
34973 34973 SRR32588730 SRX27895221 SRS24266225 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M B   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:brain|BioSampleModel:Model organism or animal                 Iso Seq RNA from brain C2 F2 M B C2 F2 M B The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240904_192359_s4.skera.flnc.fastq.gz fastq 64391727308.0 29612753.0 m84270 240904 192359 s4.skera.flnc.fastq.gz 0:2174.46 A:18972670876;C:13388478305;G:13738034427;T:18292543700;N:0 2174       18972670876 13388478305 13738034427 18292543700 0 SRX27895221 SRS24266225 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 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
36363 36363 SRR489486 SRX143563 SRS310284 SRP012376 PRJNA160143 Extensive alternative polyadenylation during zebrafish development GSE37453 Transcriptome Analysis The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome   pubmed:22722342   3P Seq Brain GSM919969   source name:mixed gender adults|genotype/variation:wild type|tissue:brain|development stage:adult 3P Seq Brain For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the … mixed gender adults Anesthetized decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at 80C. 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html Zebrafish embryos or adults grown under standard condition genotype/variation:wild type|tissue:brain|developmental stage:adult GSM919969 GSM919969: 3P Seq Brain; Danio rerio; RNA Seq GSM919969 1 GSM919969: 3P Seq Brain 1   GEO Accession:GSM919969 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <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> SRP012376     3P_Seq_Brain.fastq fastq 592119324.0 16447759.0 GSM919969 r1 0:36 A:231026484;C:109822201;G:93671127;T:157421018;N:178494 36       231026484 109822201 93671127 157421018 178494 SRX143563 SRS310284 SRA051955 GEO Whitehead Institute for Biomedical Research 1 0.57742   0.10125   0.78267   0.52634   36   B   usable mapping rate illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United States 2012-04-20 Adult Adult Brain Nervous System
37924 37924 SRR1554486 SRX685392 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF2_Brain_3.fq.gz fastq 1211892536.0 11998936.0 Brain2 Run3 0:101 A:374228993;C:286134640;G:253944548;T:297038575;N:545780 101       374228993 286134640 253944548 297038575 545780 SRX685392 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37928 37928 SRR1554474 SRX685388 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF1_Brain_3.fq.gz fastq 1192445794.0 11806394.0 Brain1 Run3 0:101 A:369786121;C:268557682;G:265557417;T:288006805;N:537769 101       369786121 268557682 265557417 288006805 537769 SRX685388 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37935 37935 SRR1554484 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Brain_1.fq.gz fastq 654412671.0 12831621.0 Brain2 Run1 0:51 A:160544180;C:166355290;G:168608762;T:158684308;N:220131 51       160544180 166355290 168608762 158684308 220131 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   0.0   0.99993   1.0   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37936 37936 SRR1554485 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Brain_2.fq.gz fastq 856322793.0 16790643.0 Brain2 Run2 0:51 A:210706815;C:226772546;G:212404752;T:201722093;N:4716587 51       210706815 226772546 212404752 201722093 4716587 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37943 37943 SRR1554472 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Brain_1.fq.gz fastq 679860294.0 13330594.0 Brain1 Run1 0:51 A:167202435;C:176450132;G:174468721;T:161497185;N:241821 51       167202435 176450132 174468721 161497185 241821 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37944 37944 SRR1554473 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Brain_2.fq.gz fastq 838372782.0 16438682.0 Brain1 Run2 0:51 A:206906228;C:221202670;G:210716690;T:195319694;N:4227500 51       206906228 221202670 210716690 195319694 4227500 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
38014 38014 SRR1265742 SRX529137 SRS598834 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Brain Replicate 3 sRNAseq GSM1376625   source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain Female Brain Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376625 GSM1376625: Female Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376625   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376625 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB012_CTTGTA_L007_R1.fastq.gz fastq 657620928.0 12894528.0 GSM1376625 r1 0:51 A:127428594;C:157315630;G:203096060;T:169719399;N:61245 51       127428594 157315630 203096060 169719399 61245 SRX529137 SRS598834 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01165   0.00109   0.99622   0.72322   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38015 38015 SRR1265741 SRX529136 SRS598833 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Brain Replicate 2 sRNAseq GSM1376624   source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain Female Brain Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376624 GSM1376624: Female Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376624   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376624 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB011_GGCTAC_L007_R1.fastq.gz fastq 197790903.0 3878253.0 GSM1376624 r1 0:51 A:39219508;C:48781853;G:60339090;T:49430999;N:19453 51       39219508 48781853 60339090 49430999 19453 SRX529136 SRS598833 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00227   0.00019   0.99835   0.67164   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38016 38016 SRR1265740 SRX529135 SRS598832 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Brain Replicate 1 sRNAseq GSM1376623   source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain Female Brain Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376623 GSM1376623: Female Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376623   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376623 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB010_TAGCTT_L007_R1.fastq.gz fastq 127765710.0 2505210.0 GSM1376623 r1 0:51 A:24845648;C:31103830;G:38874684;T:32929436;N:12112 51       24845648 31103830 38874684 32929436 12112 SRX529135 SRS598832 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.02647   0.00307   0.99368   0.59472   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38017 38017 SRR1265739 SRX529134 SRS598831 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Brain Replicate 3 sRNAseq GSM1376622   source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain Male Brain Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376622 GSM1376622: Male Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376622   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376622 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB009_TTAGGC_L007_R1.fastq.gz fastq 749856876.0 14703076.0 GSM1376622 r1 0:51 A:142133111;C:197021938;G:231006890;T:179625504;N:69433 51       142133111 197021938 231006890 179625504 69433 SRX529134 SRS598831 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00196   0.00026   0.99843   0.64615   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38018 38018 SRR1265738 SRX529133 SRS598830 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Brain Replicate 2 sRNAseq GSM1376621   source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain Male Brain Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376621 GSM1376621: Male Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376621   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376621 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB008_CGATGT_L007_R1.fastq.gz fastq 394620558.0 7737658.0 GSM1376621 r1 0:51 A:68213140;C:110690478;G:127130285;T:88550429;N:36226 51       68213140 110690478 127130285 88550429 36226 SRX529133 SRS598830 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.06427   0.00768   0.98859   0.77971   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38019 38019 SRR1265737 SRX529132 SRS598829 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Brain Replicate 1 sRNAseq GSM1376620   source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain Male Brain Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376620 GSM1376620: Male Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376620   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376620 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZB007_ATCACG_L007_R1.fastq.gz fastq 329742489.0 6465539.0 GSM1376620 r1 0:51 A:60032454;C:91021987;G:104188224;T:74471433;N:28391 51       60032454 91021987 104188224 74471433 28391 SRX529132 SRS598829 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00994   0.00098   0.99738   0.77713   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38228 38228 SRR1565820 SRX692872 SRS694598 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   HSB male rep2 GSM1496860   tissue:whole brain|strain:High Stationary Behavior|Sex:male|age:17 weeks HSB male rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:High Stationary Behavior|Sex:male|age:17 weeks GSM1496860 GSM1496860: HSB male rep2; Danio rerio; RNA Seq GSM1496860   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496860 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     hsbm2.combined.fastq fastq 3059139324.0 44987343.0 GSM1496860 r1 0:68 A:856889933;C:683001073;G:664047004;T:854889841;N:311473 68       856889933 683001073 664047004 854889841 311473 SRX692872 SRS694598 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91541   0.1123   0.71194   0.51402   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38229 38229 SRR1565819 SRX692871 SRS694597 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   HSB male rep1 GSM1496859   tissue:whole brain|strain:High Stationary Behavior|Sex:male|age:17 weeks HSB male rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:High Stationary Behavior|Sex:male|age:17 weeks GSM1496859 GSM1496859: HSB male rep1; Danio rerio; RNA Seq GSM1496859   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496859 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     hsbm1.combined.fastq fastq 4119155012.0 60575809.0 GSM1496859 r1 0:68 A:1142713472;C:928735770;G:909202318;T:1138084541;N:418911 68       1142713472 928735770 909202318 1138084541 418911 SRX692871 SRS694597 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91626   0.10986   0.71027   0.51436   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38230 38230 SRR1565818 SRX692870 SRS694596 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   HSB female rep2 GSM1496858   tissue:whole brain|strain:High Stationary Behavior|Sex:female|age:17 weeks HSB female rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:High Stationary Behavior|Sex:female|age:17 weeks GSM1496858 GSM1496858: HSB female rep2; Danio rerio; RNA Seq GSM1496858   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496858 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     hsbf2.combined.fastq fastq 2322256780.0 34150835.0 GSM1496858 r1 0:68 A:652886524;C:515567581;G:502432518;T:651135720;N:234437 68       652886524 515567581 502432518 651135720 234437 SRX692870 SRS694596 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91476   0.11796   0.70983   0.51225   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38231 38231 SRR1565817 SRX692869 SRS694595 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   HSB female rep1 GSM1496857   tissue:whole brain|strain:High Stationary Behavior|Sex:female|age:17 weeks HSB female rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:High Stationary Behavior|Sex:female|age:17 weeks GSM1496857 GSM1496857: HSB female rep1; Danio rerio; RNA Seq GSM1496857   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496857 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     hsbf1.combined.fastq fastq 3760288004.0 55298353.0 GSM1496857 r1 0:68 A:1032777273;C:857978859;G:843770671;T:1025375295;N:385906 68       1032777273 857978859 843770671 1025375295 385906 SRX692869 SRS694595 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.9211   0.11065   0.71139   0.52798   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38232 38232 SRR1565816 SRX692868 SRS694594 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   LSB male rep2 GSM1496856   tissue:whole brain|strain:Low Stationary Behavior|Sex:male|age:17 weeks LSB male rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Low Stationary Behavior|Sex:male|age:17 weeks GSM1496856 GSM1496856: LSB male rep2; Danio rerio; RNA Seq GSM1496856   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496856 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     lsbm2.combined.fastq fastq 3620479800.0 53242350.0 GSM1496856 r1 0:68 A:1012281079;C:808037554;G:792170057;T:1007622036;N:369074 68       1012281079 808037554 792170057 1007622036 369074 SRX692868 SRS694594 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91727   0.10852   0.71161   0.51898   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38233 38233 SRR1565815 SRX692867 SRS694593 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   LSB male rep1 GSM1496855   tissue:whole brain|strain:Low Stationary Behavior|Sex:male|age:17 weeks LSB male rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Low Stationary Behavior|Sex:male|age:17 weeks GSM1496855 GSM1496855: LSB male rep1; Danio rerio; RNA Seq GSM1496855   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496855 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     lsbm1.combined.fastq fastq 3939102572.0 57927979.0 GSM1496855 r1 0:68 A:1092436127;C:887516211;G:870661049;T:1088088575;N:400610 68       1092436127 887516211 870661049 1088088575 400610 SRX692867 SRS694593 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91978   0.10214   0.70869   0.5206   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38234 38234 SRR1565814 SRX692866 SRS694592 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   LSB female rep2 GSM1496854   tissue:whole brain|strain:Low Stationary Behavior|Sex:female|age:17 weeks LSB female rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Low Stationary Behavior|Sex:female|age:17 weeks GSM1496854 GSM1496854: LSB female rep2; Danio rerio; RNA Seq GSM1496854   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496854 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     lsbf2.combined.fastq fastq 3396163712.0 49943584.0 GSM1496854 r1 0:68 A:952427292;C:755558175;G:739625271;T:948206206;N:346768 68       952427292 755558175 739625271 948206206 346768 SRX692866 SRS694592 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91971   0.09762   0.7139   0.53907   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38235 38235 SRR1565813 SRX692865 SRS694591 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   LSB female rep1 GSM1496853   tissue:whole brain|strain:Low Stationary Behavior|Sex:female|age:17 weeks LSB female rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Low Stationary Behavior|Sex:female|age:17 weeks GSM1496853 GSM1496853: LSB female rep1; Danio rerio; RNA Seq GSM1496853   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496853 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     lsbf1.combined.fastq fastq 2990889832.0 43983674.0 GSM1496853 r1 0:68 A:834325179;C:670514335;G:655478374;T:830265381;N:306563 68       834325179 670514335 655478374 830265381 306563 SRX692865 SRS694591 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91961   0.10554   0.71058   0.54194   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38236 38236 SRR1565812 SRX692864 SRS694590 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   SH male rep2 GSM1496852   tissue:whole brain|strain:Scientific Hatcheries|Sex:male|age:17 weeks SH male rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Scientific Hatcheries|Sex:male|age:17 weeks GSM1496852 GSM1496852: SH male rep2; Danio rerio; RNA Seq GSM1496852   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496852 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     shm2.combined.fastq fastq 3027917260.0 44528195.0 GSM1496852 r1 0:68 A:849520890;C:674435387;G:655632316;T:848019818;N:308849 68       849520890 674435387 655632316 848019818 308849 SRX692864 SRS694590 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91854   0.11844   0.70914   0.52599   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38237 38237 SRR1565811 SRX692863 SRS694589 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   SH male rep1 GSM1496851   tissue:whole brain|strain:Scientific Hatcheries|Sex:male|age:17 weeks SH male rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Scientific Hatcheries|Sex:male|age:17 weeks GSM1496851 GSM1496851: SH male rep1; Danio rerio; RNA Seq GSM1496851   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496851 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     shm1.combined.fastq fastq 4020657964.0 59127323.0 GSM1496851 r1 0:68 A:1118924354;C:902394021;G:884260445;T:1114671095;N:408049 68       1118924354 902394021 884260445 1114671095 408049 SRX692863 SRS694589 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92006   0.11336   0.70757   0.52355   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38238 38238 SRR1565810 SRX692862 SRS694588 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   SH female rep2 GSM1496850   tissue:whole brain|strain:Scientific Hatcheries|Sex:female|age:17 weeks SH female rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Scientific Hatcheries|Sex:female|age:17 weeks GSM1496850 GSM1496850: SH female rep2; Danio rerio; RNA Seq GSM1496850   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496850 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     shf2.combined.fastq fastq 4142523076.0 60919457.0 GSM1496850 r1 0:68 A:1153819987;C:929925663;G:908337889;T:1150019261;N:420276 68       1153819987 929925663 908337889 1150019261 420276 SRX692862 SRS694588 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.91937   0.1168   0.70936   0.50937   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38239 38239 SRR1565809 SRX692861 SRS694587 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   SH female rep1 GSM1496849   tissue:whole brain|strain:Scientific Hatcheries|Sex:female|age:17 weeks SH female rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:Scientific Hatcheries|Sex:female|age:17 weeks GSM1496849 GSM1496849: SH female rep1; Danio rerio; RNA Seq GSM1496849   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496849 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     shf1.combined.fastq fastq 4453572076.0 65493707.0 GSM1496849 r1 0:68 A:1240033407;C:999435900;G:979449791;T:1234195169;N:457809 68       1240033407 999435900 979449791 1234195169 457809 SRX692861 SRS694587 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92108   0.11284   0.70678   0.52548   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38240 38240 SRR1565808 SRX692860 SRS694586 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   AB male rep2 GSM1496848   tissue:whole brain|strain:AB|Sex:male|age:17 weeks AB male rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:AB|Sex:male|age:17 weeks GSM1496848 GSM1496848: AB male rep2; Danio rerio; RNA Seq GSM1496848   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496848 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     abm2.combined.fastq fastq 2872717120.0 42245840.0 GSM1496848 r1 0:68 A:804944428;C:640905199;G:622289037;T:804286004;N:292452 68       804944428 640905199 622289037 804286004 292452 SRX692860 SRS694586 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92023   0.11215   0.71133   0.51311   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38241 38241 SRR1565807 SRX692859 SRS694585 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   AB male rep1 GSM1496847   tissue:whole brain|strain:AB|Sex:male|age:17 weeks AB male rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:AB|Sex:male|age:17 weeks GSM1496847 GSM1496847: AB male rep1; Danio rerio; RNA Seq GSM1496847   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496847 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     abm1.combined.fastq fastq 3563207208.0 52400106.0 GSM1496847 r1 0:68 A:995828497;C:796660231;G:778836484;T:991520791;N:361205 68       995828497 796660231 778836484 991520791 361205 SRX692859 SRS694585 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92353   0.10674   0.70918   0.52999   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38242 38242 SRR1565806 SRX692858 SRS694584 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   AB female rep2 GSM1496846   tissue:whole brain|strain:AB|Sex:female|age:17 weeks AB female rep2 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:AB|Sex:female|age:17 weeks GSM1496846 GSM1496846: AB female rep2; Danio rerio; RNA Seq GSM1496846   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496846 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     abf2.combined.fastq fastq 3300678452.0 48539389.0 GSM1496846 r1 0:68 A:924872216;C:737186484;G:715434941;T:922846788;N:338023 68       924872216 737186484 715434941 922846788 338023 SRX692858 SRS694584 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92017   0.11305   0.7082   0.50792   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38243 38243 SRR1565805 SRX692857 SRS694583 SRP046222 PRJNA260259 Neurotranscriptome profiles of four zebrafish strains GSE61108 Transcriptome Analysis Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subseque…   pubmed:25326170;pubmed:26032017;pubmed:26309813   AB female rep1 GSM1496845   tissue:whole brain|strain:AB|Sex:female|age:17 weeks AB female rep1 Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample whole brain   Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA   strain:AB|Sex:female|age:17 weeks GSM1496845 GSM1496845: AB female rep1; Danio rerio; RNA Seq GSM1496845   1 Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA GEO Accession:GSM1496845 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP046222     abf1.combined.fastq fastq 4306679496.0 63333522.0 GSM1496845 r1 0:68 A:1203446722;C:961797198;G:943144171;T:1197856637;N:434768 68       1203446722 961797198 943144171 1197856637 434768 SRX692857 SRS694583 SRA181596 GEO Biology, University of Nebraska at Omaha 1 0.92127   0.1098   0.70757   0.50805   68   B   usable mapping rate illumina early_illumina full_length random_priming trueseq bulk unknown unknown   United States 2014-09-04 Adult Adult Brain Nervous System
38281 38281 SRR1611974 SRX732528 SRS721348 SRP048902 PRJNA263811 Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf GSE62273 Transcriptome Analysis We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.       8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GSM1524335   tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:3 8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf   Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts. genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:3 GSM1524335 GSM1524335: 8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq GSM1524335   1 Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1524335 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP048902         878388453.0 17223303.0 GSM1524335 r1 0:51 A:232302914;C:211453624;G:203524178;T:231030317;N:77420 51       232302914 211453624 203524178 231030317 77420 SRX732528 SRS721348 SRA190781 GEO Leiden University, Institute of Biology Leiden 1 0.93382   0.06489   0.69871   0.43941   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2014-10-10 Larval Larval Brain Nervous System
38282 38282 SRR1611973 SRX732527 SRS721347 SRP048902 PRJNA263811 Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf GSE62273 Transcriptome Analysis We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.       7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GSM1524334   tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:2 7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf   Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts. genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:2 GSM1524334 GSM1524334: 7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq GSM1524334   1 Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1524334 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP048902         372336108.0 7300708.0 GSM1524334 r1 0:51 A:98058295;C:90306461;G:86107301;T:97818336;N:45715 51       98058295 90306461 86107301 97818336 45715 SRX732527 SRS721347 SRA190781 GEO Leiden University, Institute of Biology Leiden 1 0.93316   0.06305   0.69258   0.45864   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2014-10-10 Larval Larval Brain Nervous System
38283 38283 SRR1611972 SRX732526 SRS721346 SRP048902 PRJNA263811 Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf GSE62273 Transcriptome Analysis We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.       6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GSM1524333   tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:1 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf   Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts. genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:1 GSM1524333 GSM1524333: 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq GSM1524333   1 Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1524333 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP048902         426266619.0 8358169.0 GSM1524333 r1 0:51 A:112004069;C:103380899;G:98829082;T:112000953;N:51616 51       112004069 103380899 98829082 112000953 51616 SRX732526 SRS721346 SRA190781 GEO Leiden University, Institute of Biology Leiden 1 0.93027   0.05803   0.69493   0.45892   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2014-10-10 Larval Larval Brain Nervous System
38433 38433 SRR1821806 SRX893407 SRS859560 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain208 36m 3.75nM roten1 8w rep6 GSM1620953   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain208 36m 3.75nM roten1 8w rep6 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620953 GSM1620953: brain208 36m 3.75nM roten1 8w rep6; Danio rerio; RNA Seq GSM1620953   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620953 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain208.fastq.gz fastq 2306705950.0 46134119.0 GSM1620953 r1 0:50 A:636241272;C:516611728;G:510644879;T:638016950;N:5191121 50       636241272 516611728 510644879 638016950 5191121 SRX893407 SRS859560 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91528   0.15975   0.68972   0.50406   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38434 38434 SRR1821805 SRX893406 SRS859561 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain207 36m 3.75nM roten1 8w rep5 GSM1620952   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain207 36m 3.75nM roten1 8w rep5 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620952 GSM1620952: brain207 36m 3.75nM roten1 8w rep5; Danio rerio; RNA Seq GSM1620952   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620952 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain207.fastq.gz fastq 4144137850.0 82882757.0 GSM1620952 r1 0:50 A:1136843305;C:933236558;G:925158648;T:1139244251;N:9655088 50       1136843305 933236558 925158648 1139244251 9655088 SRX893406 SRS859561 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90727   0.15677   0.69337   0.51526   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38435 38435 SRR1821804 SRX893405 SRS859562 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain206 36m 3.75nM roten1 8w rep4 GSM1620951   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain206 36m 3.75nM roten1 8w rep4 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620951 GSM1620951: brain206 36m 3.75nM roten1 8w rep4; Danio rerio; RNA Seq GSM1620951   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620951 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain206.fastq.gz fastq 2682905100.0 53658102.0 GSM1620951 r1 0:50 A:743936961;C:601044963;G:590021623;T:747739178;N:162375 50       743936961 601044963 590021623 747739178 162375 SRX893405 SRS859562 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91613   0.16946   0.68832   0.50195   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38436 38436 SRR1821803 SRX893404 SRS859563 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain205 36m 3.75nM roten1 8w rep3 GSM1620950   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain205 36m 3.75nM roten1 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620950 GSM1620950: brain205 36m 3.75nM roten1 8w rep3; Danio rerio; RNA Seq GSM1620950   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620950 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain205.fastq.gz fastq 2157560400.0 43151208.0 GSM1620950 r1 0:50 A:599901370;C:482413446;G:470301148;T:604895547;N:48889 50       599901370 482413446 470301148 604895547 48889 SRX893404 SRS859563 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91687   0.17871   0.686   0.50634   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38437 38437 SRR1821802 SRX893403 SRS859564 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain204 36m 3.75nM roten1 8w rep2 GSM1620949   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain204 36m 3.75nM roten1 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620949 GSM1620949: brain204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq GSM1620949   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620949 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain204.fastq.gz fastq 2694973850.0 53899477.0 GSM1620949 r1 0:50 A:743344230;C:608541970;G:595308513;T:747727739;N:51398 50       743344230 608541970 595308513 747727739 51398 SRX893403 SRS859564 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91086   0.17132   0.69471   0.50107   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38438 38438 SRR1821801 SRX893402 SRS859565 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain203 36m 3.75nM roten1 8w rep1 GSM1620948   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks brain203 36m 3.75nM roten1 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620948 GSM1620948: brain203 36m 3.75nM roten1 8w rep1; Danio rerio; RNA Seq GSM1620948   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620948 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain203.fastq.gz fastq 2853634750.0 57072695.0 GSM1620948 r1 0:50 A:792033384;C:637485994;G:629768204;T:794292474;N:54694 50       792033384 637485994 629768204 794292474 54694 SRX893402 SRS859565 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91711   0.16964   0.68809   0.50902   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38439 38439 SRR1821800 SRX893401 SRS859566 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain172 36m 3.75nM roten1 3w rep5 GSM1620947   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks brain172 36m 3.75nM roten1 3w rep5 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620947 GSM1620947: brain172 36m 3.75nM roten1 3w rep5; Danio rerio; RNA Seq GSM1620947   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620947 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain172.fastq.gz fastq 1847093550.0 36941871.0 GSM1620947 r1 0:50 A:512828564;C:413023682;G:405063489;T:516143305;N:34510 50       512828564 413023682 405063489 516143305 34510 SRX893401 SRS859566 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91332   0.16726   0.69219   0.50709   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38440 38440 SRR1821799 SRX893400 SRS859567 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain171 36m 3.75nM roten1 3w rep4 GSM1620946   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks brain171 36m 3.75nM roten1 3w rep4 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620946 GSM1620946: brain171 36m 3.75nM roten1 3w rep4; Danio rerio; RNA Seq GSM1620946   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620946 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain171.fastq.gz fastq 2115110500.0 42302210.0 GSM1620946 r1 0:50 A:605803255;C:456285353;G:449264746;T:603715506;N:41640 50       605803255 456285353 449264746 603715506 41640 SRX893400 SRS859567 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92083   0.15603   0.71752   0.53696   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38441 38441 SRR1821798 SRX893399 SRS859568 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain170 36m 3.75nM roten1 3w rep3 GSM1620945   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks brain170 36m 3.75nM roten1 3w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620945 GSM1620945: brain170 36m 3.75nM roten1 3w rep3; Danio rerio; RNA Seq GSM1620945   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620945 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain170.fastq.gz fastq 1954824850.0 39096497.0 GSM1620945 r1 0:50 A:550573629;C:429779639;G:422566533;T:551846246;N:58803 50       550573629 429779639 422566533 551846246 58803 SRX893399 SRS859568 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91485   0.15534   0.69863   0.51851   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38442 38442 SRR1821797 SRX893398 SRS859569 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain169 36m 3.75nM roten1 3w rep2 GSM1620944   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks brain169 36m 3.75nM roten1 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620944 GSM1620944: brain169 36m 3.75nM roten1 3w rep2; Danio rerio; RNA Seq GSM1620944   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620944 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain169.fastq.gz fastq 1849506700.0 36990134.0 GSM1620944 r1 0:50 A:515047742;C:412800018;G:402098235;T:518926309;N:634396 50       515047742 412800018 402098235 518926309 634396 SRX893398 SRS859569 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91857   0.1714   0.69069   0.53039   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38443 38443 SRR1821796 SRX893397 SRS859570 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain168 36m 3.75nM roten1 3w rep1 GSM1620943   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks brain168 36m 3.75nM roten1 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620943 GSM1620943: brain168 36m 3.75nM roten1 3w rep1; Danio rerio; RNA Seq GSM1620943   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620943 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain168.fastq.gz fastq 2080177550.0 41603551.0 GSM1620943 r1 0:50 A:581188271;C:463464308;G:451483040;T:583963411;N:78520 50       581188271 463464308 451483040 583963411 78520 SRX893397 SRS859570 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91585   0.1671   0.69487   0.51506   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38444 38444 SRR1821795 SRX893396 SRS859571 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain188 36m control 8w rep4 GSM1620942   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks brain188 36m control 8w rep4 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:8 weeks GSM1620942 GSM1620942: brain188 36m control 8w rep4; Danio rerio; RNA Seq GSM1620942   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620942 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain188.fastq.gz fastq 2159431000.0 43188620.0 GSM1620942 r1 0:50 A:600353952;C:482641833;G:469939355;T:606303730;N:192130 50       600353952 482641833 469939355 606303730 192130 SRX893396 SRS859571 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91749   0.16727   0.69694   0.53135   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38445 38445 SRR1821794 SRX893395 SRS859572 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain187 36m control 8w rep3 GSM1620941   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks brain187 36m control 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:8 weeks GSM1620941 GSM1620941: brain187 36m control 8w rep3; Danio rerio; RNA Seq GSM1620941   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620941 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain187.fastq.gz fastq 2146914450.0 42938289.0 GSM1620941 r1 0:50 A:593471539;C:482978847;G:475357906;T:594986562;N:119596 50       593471539 482978847 475357906 594986562 119596 SRX893395 SRS859572 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91579   0.16487   0.69696   0.50805   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38446 38446 SRR1821793 SRX893394 SRS859573 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain186 36m control 8w rep2 GSM1620940   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks brain186 36m control 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:8 weeks GSM1620940 GSM1620940: brain186 36m control 8w rep2; Danio rerio; RNA Seq GSM1620940   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620940 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain186.fastq.gz fastq 1892437850.0 37848757.0 GSM1620940 r1 0:50 A:529236009;C:421442136;G:411249794;T:530397650;N:112261 50       529236009 421442136 411249794 530397650 112261 SRX893394 SRS859573 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91541   0.17265   0.69394   0.5234   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38447 38447 SRR1821792 SRX893393 SRS859574 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain185 36m control 8w rep1 GSM1620939   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks brain185 36m control 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:8 weeks GSM1620939 GSM1620939: brain185 36m control 8w rep1; Danio rerio; RNA Seq GSM1620939   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620939 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain185.fastq.gz fastq 2412353350.0 48247067.0 GSM1620939 r1 0:50 A:667642370;C:540578365;G:531795577;T:672286916;N:50122 50       667642370 540578365 531795577 672286916 50122 SRX893393 SRS859574 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9171   0.15741   0.6929   0.52634   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38448 38448 SRR1821791 SRX893392 SRS859575 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain162 36m control 3w rep3 GSM1620938   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks brain162 36m control 3w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:3 weeks GSM1620938 GSM1620938: brain162 36m control 3w rep3; Danio rerio; RNA Seq GSM1620938   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620938 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain162.fastq.gz fastq 2115792900.0 42315858.0 GSM1620938 r1 0:50 A:591284907;C:470346585;G:459440113;T:594665906;N:55389 50       591284907 470346585 459440113 594665906 55389 SRX893392 SRS859575 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91262   0.18165   0.69175   0.49864   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38449 38449 SRR1821790 SRX893391 SRS859576 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain161 36m control 3w rep2 GSM1620937   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks brain161 36m control 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:3 weeks GSM1620937 GSM1620937: brain161 36m control 3w rep2; Danio rerio; RNA Seq GSM1620937   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620937 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain161.fastq.gz fastq 3008253050.0 60165061.0 GSM1620937 r1 0:50 A:837622392;C:671074775;G:660143820;T:839331178;N:80885 50       837622392 671074775 660143820 839331178 80885 SRX893391 SRS859576 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91262   0.16992   0.69497   0.5073   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38450 38450 SRR1821789 SRX893390 SRS859577 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain160 36m control 3w rep1 GSM1620936   source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks brain160 36m control 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:36 month|treatment:n1|duration:3 weeks GSM1620936 GSM1620936: brain160 36m control 3w rep1; Danio rerio; RNA Seq GSM1620936   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620936 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain160.fastq.gz fastq 2276421850.0 45528437.0 GSM1620936 r1 0:50 A:635790951;C:504584896;G:496496426;T:639505870;N:43707 50       635790951 504584896 496496426 639505870 43707 SRX893390 SRS859577 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91459   0.17586   0.69501   0.52684   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38451 38451 SRR1821788 SRX893389 SRS859578 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain184 12m control 8w rep3 GSM1620935   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks brain184 12m control 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:8 weeks GSM1620935 GSM1620935: brain184 12m control 8w rep3; Danio rerio; RNA Seq GSM1620935   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620935 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain184.fastq.gz fastq 2278129750.0 45562595.0 GSM1620935 r1 0:50 A:631799307;C:510023581;G:500313528;T:635941275;N:52059 50       631799307 510023581 500313528 635941275 52059 SRX893389 SRS859578 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91986   0.1596   0.69716   0.51685   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38452 38452 SRR1821787 SRX893388 SRS859579 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain183 12m control 8w rep2 GSM1620934   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks brain183 12m control 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:8 weeks GSM1620934 GSM1620934: brain183 12m control 8w rep2; Danio rerio; RNA Seq GSM1620934   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620934 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain183.fastq.gz fastq 2224353800.0 44487076.0 GSM1620934 r1 0:50 A:618322260;C:496812855;G:486578426;T:622597552;N:42707 50       618322260 496812855 486578426 622597552 42707 SRX893388 SRS859579 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91707   0.16186   0.6981   0.50647   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38453 38453 SRR1821786 SRX893387 SRS859580 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain182 12m control 8w rep1 GSM1620933   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks brain182 12m control 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:8 weeks GSM1620933 GSM1620933: brain182 12m control 8w rep1; Danio rerio; RNA Seq GSM1620933   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620933 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain182.fastq.gz fastq 2529540100.0 50590802.0 GSM1620933 r1 0:50 A:702082535;C:564419392;G:557247066;T:705743714;N:47393 50       702082535 564419392 557247066 705743714 47393 SRX893387 SRS859580 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.919   0.1675   0.69542   0.51245   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38454 38454 SRR1821785 SRX893386 SRS859581 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain159 12m control 3w rep3 GSM1620932   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks brain159 12m control 3w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:3 weeks GSM1620932 GSM1620932: brain159 12m control 3w rep3; Danio rerio; RNA Seq GSM1620932   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620932 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain159.fastq.gz fastq 1852400050.0 37048001.0 GSM1620932 r1 0:50 A:516159124;C:413012844;G:403938874;T:519233327;N:55881 50       516159124 413012844 403938874 519233327 55881 SRX893386 SRS859581 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91641   0.1728   0.6911   0.51585   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38455 38455 SRR1821784 SRX893385 SRS859582 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain158 12m control 3w rep2 GSM1620931   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks brain158 12m control 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:3 weeks GSM1620931 GSM1620931: brain158 12m control 3w rep2; Danio rerio; RNA Seq GSM1620931   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620931 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain158.fastq.gz fastq 1909179250.0 38183585.0 GSM1620931 r1 0:50 A:530445060;C:427180963;G:415243468;T:534710201;N:1599558 50       530445060 427180963 415243468 534710201 1599558 SRX893385 SRS859582 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91943   0.17238   0.69459   0.50393   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
38456 38456 SRR1821783 SRX893384 SRS859583 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   brain157 12m control 3w rep1 GSM1620930   source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks brain157 12m control 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from brain Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:brain|age:12 month|treatment:n1|duration:3 weeks GSM1620930 GSM1620930: brain157 12m control 3w rep1; Danio rerio; RNA Seq GSM1620930   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620930 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Brain157.fastq.gz fastq 2407579650.0 48151593.0 GSM1620930 r1 0:50 A:670537335;C:536499860;G:527478669;T:672973571;N:90215 50       670537335 536499860 527478669 672973571 90215 SRX893384 SRS859583 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91661   0.16668   0.69538   0.5014   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Brain Nervous System
39625 39625 SRR1920171 SRX960487 SRS877482 SRP056356 PRJNA278935 Transcriptome profiling from the brain of male and female zebrafish GSE67092 Transcriptome Analysis Genome wide analysis to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.       RZB0003 Female GSM1638735   source name:Female brain tissue|genotype:Wild type|Sex:female|tissue:Brain RZB0003 Female Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication quality threshold <= 30 and loaded to Genespring NGS Reads per kilobase per megabase RPKM was calculated and normalized using the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample. Female brain tissue   Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.   genotype:Wild type|Sex:female|tissue:Brain GSM1638735 GSM1638735: RZB0003 Female; Danio rerio; RNA Seq GSM1638735   1 Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length. GEO Accession:GSM1638735 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP056356     RZB003_NoIndex_L004_R1_All.fastq.gz fastq 14531005592.0 191197442.0 GSM1638735 r1 0:76 A:4108884359;C:3166835425;G:3143573307;T:4098665685;N:13046816 76       4108884359 3166835425 3143573307 4098665685 13046816 SRX960487 SRS877482 SRA247878 GEO Computational and Systems Biology, Genome Institute of Singapore 1 0.91338   0.17886   0.69049   0.5006   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Singapore 2015-03-20 Undetermined Undetermined Brain Nervous System
39626 39626 SRR1920170 SRX960486 SRS877483 SRP056356 PRJNA278935 Transcriptome profiling from the brain of male and female zebrafish GSE67092 Transcriptome Analysis Genome wide analysis to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.       RZB0002 Male GSM1638734   source name:Male brain tissue|genotype:Wild type|Sex:male|tissue:Brain RZB0002 Male Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication quality threshold <= 30 and loaded to Genespring NGS Reads per kilobase per megabase RPKM was calculated and normalized using the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample. Male brain tissue   Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.   genotype:Wild type|Sex:male|tissue:Brain GSM1638734 GSM1638734: RZB0002 Male; Danio rerio; RNA Seq GSM1638734   1 Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length. GEO Accession:GSM1638734 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP056356     RZB002_NoIndex_L001_R1_All.fastq.gz fastq 14711238148.0 193568923.0 GSM1638734 r1 0:76 A:4154125162;C:3219757523;G:3187842434;T:4138123659;N:11389370 76       4154125162 3219757523 3187842434 4138123659 11389370 SRX960486 SRS877483 SRA247878 GEO Computational and Systems Biology, Genome Institute of Singapore 1 0.91063   0.20427   0.70183   0.50769   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Singapore 2015-03-20 Undetermined Undetermined 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

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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");;