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476 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Surface Structure"

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experiment.library_selection 10

devstage_curation 8

devstage_curation_coarse 6

tissue_curation 4

experiment.platform 4

experiment.library_strategy 4

tissue_curation_coarse 1

  • Surface Structure · 476 ✖

technology 1

  • unknown · 476 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 476 ✖
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
95 95 DRR050167 DRX045209 DRS025834 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 3 SAMD00044057   sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044057 DRX045209 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044057       371748120.0 3469843.0 DRR050167 0:107.14 A:107190409;C:79475572;G:83520360;T:101561779;N:0 107       107190409 79475572 83520360 101561779 0 DRX045209 DRS025834 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.81026   0.26715   0.86953   0.52321   51   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
96 96 DRR050166 DRX045208 DRS025833 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 2 SAMD00044056   sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044056 DRX045208 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044056       425549011.0 3275261.0 DRR050166 0:129.93 A:126640704;C:86415371;G:90822163;T:121670773;N:0 129       126640704 86415371 90822163 121670773 0 DRX045208 DRS025833 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80223   0.31429   0.85861   0.5272   57   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
97 97 DRR050165 DRX045207 DRS025832 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 1 SAMD00044055   sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044055 DRX045207 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044055       584599765.0 3941083.0 DRR050165 0:148.33 A:164329030;C:129885620;G:136727379;T:153657736;N:0 148       164329030 129885620 136727379 153657736 0 DRX045207 DRS025832 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.83769   0.25395   0.83116   0.52784   185   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
98 98 DRR050164 DRX045206 DRS025831 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 3 SAMD00044054   sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044054 DRX045206 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044054       343014114.0 3827762.0 DRR050164 0:89.61 A:99421434;C:73070267;G:77738821;T:92783592;N:0 89       99421434 73070267 77738821 92783592 0 DRX045206 DRS025831 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.78953   0.25529   0.87367   0.52148   24   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
99 99 DRR050163 DRX045205 DRS025830 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 2 SAMD00044053   sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044053 DRX045205 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044053       533069427.0 3824140.0 DRR050163 0:139.40 A:152608173;C:113928273;G:120051739;T:146481242;N:0 139       152608173 113928273 120051739 146481242 0 DRX045205 DRS025830 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80412   0.26768   0.85338   0.52255   245   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
100 100 DRR050162 DRX045204 DRS025829 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 1 SAMD00044052   sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044052 DRX045204 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044052       478262965.0 4224064.0 DRR050162 0:113.22 A:136348264;C:104872341;G:113114502;T:123927858;N:0 113       136348264 104872341 113114502 123927858 0 DRX045204 DRS025829 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.86947   0.29839   0.83317   0.51453   80   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
125 125 DRR189379 DRX179844 DRS200410 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 3 SAMD00182222   sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182222 DRX179844 Emx3 / Larva body 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 SAMD00182222       1759409208.0 48872478.0 DRR189379 0:36 A:401147348;C:424523813;G:426350919;T:507310828;N:76300 36       401147348 424523813 426350919 507310828 76300 DRX179844 DRS200410 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90975   0.11439   0.66076   0.47775   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
126 126 DRR189378 DRX179843 DRS200409 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 2 SAMD00182221   sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182221 DRX179843 Emx3 / Larva body 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 SAMD00182221       1318201020.0 36616695.0 DRR189378 0:36 A:297850068;C:316786585;G:323717530;T:379789606;N:57231 36       297850068 316786585 323717530 379789606 57231 DRX179843 DRS200409 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.9116   0.11269   0.65837   0.46733   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
127 127 DRR189377 DRX179842 DRS200408 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 1 SAMD00182220   sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182220 DRX179842 Emx3 / Larva body 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 SAMD00182220       812483964.0 22568999.0 DRR189377 0:36 A:185173338;C:197790160;G:197482964;T:232000884;N:36618 36       185173338 197790160 197482964 232000884 36618 DRX179842 DRS200408 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91107   0.1171   0.65981   0.47458   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
128 128 DRR189376 DRX179841 DRS200449 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 3 SAMD00182219   sample name:WT Larva body 3|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182219 DRX179841 WT Larva body 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 SAMD00182219       4030038144.0 111945504.0 DRR189376 0:36 A:943709984;C:971756680;G:977594500;T:1136798448;N:178532 36       943709984 971756680 977594500 1136798448 178532 DRX179841 DRS200449 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89574   0.12331   0.65831   0.48096   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
129 129 DRR189375 DRX179840 DRS200448 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 2 SAMD00182218   sample name:WT Larva body 2|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182218 DRX179840 WT Larva body 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 SAMD00182218       1991670804.0 55324189.0 DRR189375 0:36 A:454367176;C:479012055;G:488407231;T:569793674;N:90668 36       454367176 479012055 488407231 569793674 90668 DRX179840 DRS200448 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90911   0.12455   0.65494   0.47971   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
130 130 DRR189374 DRX179839 DRS200447 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 1 SAMD00182217   sample name:WT Larva body 1|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182217 DRX179839 WT Larva body 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 SAMD00182217       1018340100.0 28287225.0 DRR189374 0:36 A:233370050;C:244140659;G:247795084;T:292989542;N:44765 36       233370050 244140659 247795084 292989542 44765 DRX179839 DRS200447 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91078   0.12578   0.6524   0.48016   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
173 173 DRR075397 DRX069311 DRS075492 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The remaining part of body of control fish 7dpf Control body SAMD00065411   sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body                 Illumina HiSeq 2500 sequencing of SAMD00065411 DRX069311 Control body 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <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> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065411       2653100352.0 73697232.0 DRR075397 0:36 A:656791658;C:620507513;G:625038612;T:750671135;N:91434 36       656791658 620507513 625038612 750671135 91434 DRX069311 DRS075492 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.89666   0.15749   0.67048   0.47755   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Trunk Surface Structure
282 282 DRR179616 DRX170142 DRS185505 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin xanthophore 03 SAMD00172019   sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172019 DRX170142 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172019       376558775.0 1624500.0 DRR179616 0:231.80 A:107837072;C:79508449;G:79372899;T:109840355;N:0 231       107837072 79508449 79372899 109840355 0 DRX170142 DRS185505 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.86944   0.10951   0.90425   0.59385   311   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
283 283 DRR179615 DRX170141 DRS185504 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 02 SAMD00172018   sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172018 DRX170141 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172018       515115515.0 2124170.0 DRR179615 0:242.50 A:138421982;C:119032803;G:119412227;T:138248503;N:0 242       138421982 119032803 119412227 138248503 0 DRX170141 DRS185504 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88998   0.05858   0.88051   0.50917   284   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
284 284 DRR179614 DRX170140 DRS185503 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 01 SAMD00172017   sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172017 DRX170140 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172017       371242152.0 1504407.0 DRR179614 0:246.77 A:99341086;C:86126839;G:86264882;T:99509345;N:0 246       99341086 86126839 86264882 99509345 0 DRX170140 DRS185503 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88672   0.06422   0.85679   0.5066   56   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
285 285 DRR179613 DRX170139 DRS185502 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin melanophore 03 SAMD00172016   sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172016 DRX170139 Zebrafish fin melanophore 03 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172016       342802993.0 1585538.0 DRR179613 0:216.21 A:90833658;C:80789744;G:80463233;T:90716358;N:0 216       90833658 80789744 80463233 90716358 0 DRX170139 DRS185502 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.8312   0.03528   0.88605   0.47299   285   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
286 286 DRR179612 DRX170138 DRS185501 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 02 SAMD00172015   sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172015 DRX170138 Zebrafish fin melanophore 02 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172015       538412675.0 2168231.0 DRR179612 0:248.32 A:147128403;C:121854818;G:121564109;T:147865345;N:0 248       147128403 121854818 121564109 147865345 0 DRX170138 DRS185501 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.89106   0.07081   0.89286   0.5935   283   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
287 287 DRR179611 DRX170137 DRS185500 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 01 SAMD00172014   sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172014 DRX170137 Zebrafish fin melanophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</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> DRP007318 Ion Torrent PGM sequencing of SAMD00172014       282446840.0 1311431.0 DRR179611 0:215.37 A:74927237;C:66575483;G:66161471;T:74782649;N:0 215       74927237 66575483 66161471 74782649 0 DRX170137 DRS185500 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.85938   0.0335   0.89248   0.58813   274   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
3759 3759 ERR1294279 ERX1365625 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9 vbu13 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu13_GCCAAT_L008_R1_001.fastq.gz fastq 2376143675.0 23526175.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9 0:101 A:655940769;C:534990399;G:527934646;T:655773043;N:1504818 101       655940769 534990399 527934646 655773043 1504818 ERX1365625 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95443   0.10666   0.73176   0.50978   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3760 3760 ERR1294278 ERX1365624 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 vbu12 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu12_GTGAAA_L008_R1_001.fastq.gz fastq 1449181835.0 14348335.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 0:101 A:399518584;C:327615685;G:323868050;T:397240465;N:939051 101       399518584 327615685 323868050 397240465 939051 ERX1365624 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95893   0.09315   0.73464   0.48744   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3761 3761 ERR1294277 ERX1365623 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 vbu11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu11_GTCCGC_L008_R1_001.fastq.gz fastq 1455235169.0 14408269.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 0:101 A:392100064;C:337980617;G:331091626;T:393178582;N:884280 101       392100064 337980617 331091626 393178582 884280 ERX1365623 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95485   0.08016   0.72845   0.47549   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3762 3762 ERR1294276 ERX1365622 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 ve13 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve13_CCGTCC_L008_R1_001.fastq.gz fastq 1029294030.0 10191030.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 0:101 A:284612731;C:231451012;G:228443320;T:284135536;N:651431 101       284612731 231451012 228443320 284135536 651431 ERX1365622 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93287   0.10726   0.72585   0.4913   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3763 3763 ERR1294275 ERX1365621 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5 ve12 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve12_ATGTCA_L008_R1_001.fastq.gz fastq 1446322222.0 14320022.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5 0:101 A:400821160;C:324210104;G:320286425;T:400078485;N:926048 101       400821160 324210104 320286425 400078485 926048 ERX1365621 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.92778   0.09489   0.73093   0.48493   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3764 3764 ERR1294274 ERX1365620 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 ve11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve11_AGTTCC_L008_R1_001.fastq.gz fastq 2117238861.0 20962761.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 0:101 A:591654664;C:469803769;G:462550117;T:591863795;N:1366516 101       591654664 469803769 462550117 591863795 1366516 ERX1365620 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93146   0.09666   0.73501   0.48749   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3765 3765 ERR1294273 ERX1365619 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3 wt3 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt3_AGTCAA_L008_R1_001.fastq.gz fastq 2631687411.0 26056311.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3 0:101 A:734843629;C:584316000;G:577487406;T:733356850;N:1683526 101       734843629 584316000 577487406 733356850 1683526 ERX1365619 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95114   0.1036   0.72474   0.48261   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3766 3766 ERR1294272 ERX1365618 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 wt2 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt2_CTTGTA_L008_R1_001.fastq.gz fastq 2093443463.0 20727163.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 0:101 A:607582034;C:442802229;G:437957089;T:603752294;N:1349817 101       607582034 442802229 437957089 603752294 1349817 ERX1365618 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.94792   0.10892   0.73277   0.51067   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3767 3767 ERR1294271 ERX1365617 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1 wt1 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt1_CAGATC_L008_R1_001.fastq.gz fastq 1701561241.0 16847141.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1 0:101 A:505358711;C:348893979;G:343445186;T:502880170;N:983195 101       505358711 348893979 343445186 502880170 983195 ERX1365617 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.94565   0.13032   0.73669   0.50473   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
9970 9970 ERR5056255 ERX4862324 ERS4959151 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198930 University of Bristol ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG3_CTTGTA_L002_R1_001.fastq.gz fastq 435534645.0 8539895.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 10 0:51 1:0 A:104994334;C:102642310;G:101303422;T:126578362;N:16217 51 0     104994334 102642310 101303422 126578362 16217 ERX4862324 ERS4959151 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.92322   0.08481   0.71997   0.45351   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9971 9971 ERR5056093 ERX4862162 ERS4959146 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198925 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT1_CGATGT_L002_R1_001.fastq.gz fastq 613101549.0 12021599.0 ena RUN BRISTOL 08 01 2021 13:16:55:212 1 0:51 1:0 A:152016801;C:139221646;G:139332264;T:182506912;N:23926 51 0     152016801 139221646 139332264 182506912 23926 ERX4862162 ERS4959146 ERA3206646 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90335   0.1072   0.71784   0.48228   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9972 9972 ERR5056077 ERX4862146 ERS4959146 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198925 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT1_CGATGT_L001_R1_001.fastq.gz fastq 600285402.0 11770302.0 ena RUN BRISTOL 08 01 2021 12:07:14:527 1 0:51 1:0 A:148729943;C:136337224;G:136545524;T:178606078;N:66633 51 0     148729943 136337224 136545524 178606078 66633 ERX4862146 ERS4959146 ERA3206631 University of Bristol|European Nucleotide Archive University of Bristol 1 0.9026   0.10732   0.71683   0.47346   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9973 9973 ERR5056254 ERX4862323 ERS4959151 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198930 University of Bristol ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG3_CTTGTA_L001_R1_001.fastq.gz fastq 426117342.0 8355242.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 9 0:51 1:0 A:102630499;C:100472291;G:99193964;T:123775368;N:45220 51 0     102630499 100472291 99193964 123775368 45220 ERX4862323 ERS4959151 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.92245   0.08463   0.71877   0.45377   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9974 9974 ERR5056253 ERX4862322 ERS4959150 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198929 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG2_CAGATC_L002_R1_001.fastq.gz fastq 434571714.0 8521014.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 8 0:51 1:0 A:106135147;C:102194661;G:100594136;T:125630448;N:17322 51 0     106135147 102194661 100594136 125630448 17322 ERX4862322 ERS4959150 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91779   0.08112   0.7161   0.4437   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9975 9975 ERR5056252 ERX4862321 ERS4959150 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198929 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG2_CAGATC_L001_R1_001.fastq.gz fastq 424788384.0 8329184.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 7 0:51 1:0 A:103644078;C:99946940;G:98381633;T:122768121;N:47612 51 0     103644078 99946940 98381633 122768121 47612 ERX4862321 ERS4959150 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91867   0.08097   0.71388   0.44882   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9976 9976 ERR5056251 ERX4862320 ERS4959149 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198928 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG1_GCCAAT_L002_R1_001.fastq.gz fastq 481725498.0 9445598.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 6 0:51 1:0 A:117075718;C:111922649;G:112057835;T:140651082;N:18214 51 0     117075718 111922649 112057835 140651082 18214 ERX4862320 ERS4959149 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91312   0.08654   0.71747   0.46716   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9977 9977 ERR5056250 ERX4862319 ERS4959149 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198928 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG1_GCCAAT_L001_R1_001.fastq.gz fastq 471197976.0 9239176.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 5 0:51 1:0 A:114367789;C:109551764;G:109678406;T:137546387;N:53630 51 0     114367789 109551764 109678406 137546387 53630 ERX4862319 ERS4959149 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91412   0.08674   0.71632   0.46601   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9978 9978 ERR5056249 ERX4862318 ERS4959148 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale SAMEA7198927 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT3_ACAGTG_L002_R1_001.fastq.gz fastq 470142531.0 9218481.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 4 0:51 1:0 A:116971308;C:106056823;G:107128214;T:139968487;N:17699 51 0     116971308 106056823 107128214 139968487 17699 ERX4862318 ERS4959148 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90722   0.1158   0.72287   0.46674   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9979 9979 ERR5056248 ERX4862317 ERS4959148 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale SAMEA7198927 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT3_ACAGTG_L001_R1_001.fastq.gz fastq 460312587.0 9025737.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 3 0:51 1:0 A:114396758;C:103865119;G:105005018;T:136994559;N:51133 51 0     114396758 103865119 105005018 136994559 51133 ERX4862317 ERS4959148 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90759   0.11359   0.7208   0.47232   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9980 9980 ERR5056247 ERX4862316 ERS4959147 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198926 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT2_TGACCA_L002_R1_001.fastq.gz fastq 502898046.0 9860746.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 2 0:51 1:0 A:123893447;C:111981365;G:116049412;T:150953220;N:20602 51 0     123893447 111981365 116049412 150953220 20602 ERX4862316 ERS4959147 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90777   0.11921   0.7137   0.48182   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9981 9981 ERR5056246 ERX4862315 ERS4959147 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198926 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT2_TGACCA_L001_R1_001.fastq.gz fastq 491866134.0 9644434.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 1 0:51 1:0 A:121063841;C:109534722;G:113610951;T:147602721;N:53899 51 0     121063841 109534722 113610951 147602721 53899 ERX4862315 ERS4959147 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.907   0.11935   0.71364   0.48543   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
32541 32541 SRR29303120 SRX24820197 SRS21534299 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 10|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 1 L6H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_1.fq.gz fastq 619966455.0 12156205.0 L6H 1.fq.gz 0:51 A:143411079;C:162001488;G:168382605;T:146007422;N:163861 51       143411079 162001488 168382605 146007422 163861 SRX24820197 SRS21534299 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01303   0.00337   0.99472   0.5628   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32542 32542 SRR29303121 SRX24820196 SRS21534298 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 09|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 3 L3H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_3.fq.gz fastq 738125703.0 14473053.0 L3H 3.fq.gz 0:51 A:176614297;C:190760467;G:197157923;T:173400138;N:192878 51       176614297 190760467 197157923 173400138 192878 SRX24820196 SRS21534298 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01163   0.00356   0.99379   0.55469   51   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32543 32543 SRR29303122 SRX24820195 SRS21534297 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 08|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 2 L3H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_2.fq.gz fastq 489154821.0 9591271.0 L3H 2.fq.gz 0:51 A:109695797;C:132121151;G:127787221;T:119539033;N:11619 51       109695797 132121151 127787221 119539033 11619 SRX24820195 SRS21534297 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.05359   0.01132   0.98924   0.55364   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32544 32544 SRR29303123 SRX24820194 SRS21534296 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 07|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 1 L3H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_1.fq.gz fastq 551502015.0 10813765.0 L3H 1.fq.gz 0:51 A:130437158;C:141969110;G:146479841;T:132605147;N:10759 51       130437158 141969110 146479841 132605147 10759 SRX24820194 SRS21534296 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.13403   0.01834   0.98735   0.54849   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32545 32545 SRR29303124 SRX24820193 SRS21534295 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 06|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 3 L1H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_3.fq.gz fastq 524533827.0 10284977.0 L1H 3.fq.gz 0:51 A:118598837;C:136729611;G:142993590;T:126201873;N:9916 51       118598837 136729611 142993590 126201873 9916 SRX24820193 SRS21534295 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.00829   0.00187   0.99472   0.54701   51   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32546 32546 SRR29303125 SRX24820192 SRS21534294 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 05|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 2 L1H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_2.fq.gz fastq 541697163.0 10621513.0 L1H 2.fq.gz 0:51 A:126751483;C:135818134;G:141122995;T:137953543;N:51008 51       126751483 135818134 141122995 137953543 51008 SRX24820192 SRS21534294 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.33438   0.08101   0.98238   0.53337   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32547 32547 SRR29303126 SRX24820191 SRS21534293 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 04|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 1 L1H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_1.fq.gz fastq 930096282.0 18237182.0 L1H 1.fq.gz 0:51 A:212568445;C:243497911;G:260145458;T:213851032;N:33436 51       212568445 243497911 260145458 213851032 33436 SRX24820191 SRS21534293 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.64143   0.02683   0.98683   0.5342   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32548 32548 SRR29303127 SRX24820190 SRS21534292 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 03|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 3 DD 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_3.fq.gz fastq 667459389.0 13087439.0 DD 3.fq.gz 0:51 A:157267065;C:168909886;G:178336724;T:162865168;N:80546 51       157267065 168909886 178336724 162865168 80546 SRX24820190 SRS21534292 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.19375   0.03528   0.98827   0.55124   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32549 32549 SRR29303128 SRX24820189 SRS21534291 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 12|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 3 L6H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_3.fq.gz fastq 551181072.0 10807472.0 L6H 3.fq.gz 0:51 A:126813056;C:141881980;G:147676363;T:134665008;N:144665 51       126813056 141881980 147676363 134665008 144665 SRX24820189 SRS21534291 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.09301   0.01507   0.99042   0.54323   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32550 32550 SRR29303129 SRX24820188 SRS21534290 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 11|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 2 L6H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_2.fq.gz fastq 571762632.0 11211032.0 L6H 2.fq.gz 0:51 A:138521192;C:148068464;G:150615597;T:134408189;N:149190 51       138521192 148068464 150615597 134408189 149190 SRX24820188 SRS21534290 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01523   0.00336   0.9933   0.57685   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32551 32551 SRR29303130 SRX24820187 SRS21534289 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 02|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 2 DD 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_2.fq.gz fastq 706940937.0 13861587.0 DD 2.fq.gz 0:51 A:162899595;C:189209828;G:187422113;T:167222837;N:186564 51       162899595 189209828 187422113 167222837 186564 SRX24820187 SRS21534289 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.02266   0.00566   0.99334   0.56959   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32552 32552 SRR29303131 SRX24820186 SRS21534288 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 01|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 1 DD 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_1.fq.gz fastq 540332862.0 10594762.0 DD 1.fq.gz 0:51 A:127336994;C:143901414;G:142437491;T:126515166;N:141797 51       127336994 143901414 142437491 126515166 141797 SRX24820186 SRS21534288 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01404   0.00313   0.99484   0.56573   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
35557 35557 SRR32880273 SRX28160884 SRS24513822 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 5 GSM8875053   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 5 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875053 GSM8875053: 3dpa blastema exercised exp bio rep 5; Danio rerio; RNA Seq GSM8875053 r1 GSM8875053 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_5_raw.fastq.gz fastq 3833406286.0 31421363.0 GSM8875053 r1 0:122 A:1051289152;C:808410920;G:908646262;T:1064964960;N:94992 122       1051289152 808410920 908646262 1064964960 94992 SRX28160884 SRS24513822 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35558 35558 SRR32880274 SRX28160883 SRS24513821 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 4 GSM8875052   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 4 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875052 GSM8875052: 3dpa blastema exercised exp bio rep 4; Danio rerio; RNA Seq GSM8875052 r1 GSM8875052 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_4_raw.fastq.gz fastq 2716320484.0 22264922.0 GSM8875052 r1 0:122 A:753716648;C:572683669;G:633777091;T:756074187;N:68889 122       753716648 572683669 633777091 756074187 68889 SRX28160883 SRS24513821 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35559 35559 SRR32880275 SRX28160882 SRS24513820 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 3 GSM8875051   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 3 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875051 GSM8875051: 3dpa blastema exercised exp bio rep 3; Danio rerio; RNA Seq GSM8875051 r1 GSM8875051 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_3_raw.fastq.gz fastq 3326494944.0 27266352.0 GSM8875051 r1 0:122 A:929692130;C:705713811;G:773972336;T:917030832;N:85835 122       929692130 705713811 773972336 917030832 85835 SRX28160882 SRS24513820 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35560 35560 SRR32880276 SRX28160881 SRS24513819 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 2 GSM8875050   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 2 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875050 GSM8875050: 3dpa blastema exercised exp bio rep 2; Danio rerio; RNA Seq GSM8875050 r1 GSM8875050 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_2_raw.fastq.gz fastq 3319809954.0 27211557.0 GSM8875050 r1 0:122 A:912008882;C:704589377;G:783108238;T:920018852;N:84605 122       912008882 704589377 783108238 920018852 84605 SRX28160881 SRS24513819 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35561 35561 SRR32880277 SRX28160880 SRS24513818 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 1 GSM8875049   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 1 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875049 GSM8875049: 3dpa blastema exercised exp bio rep 1; Danio rerio; RNA Seq GSM8875049 r1 GSM8875049 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_1_raw.fastq.gz fastq 3744436322.0 30692101.0 GSM8875049 r1 0:122 A:1050863937;C:775277972;G:866627322;T:1051571183;N:95908 122       1050863937 775277972 866627322 1051571183 95908 SRX28160880 SRS24513818 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35562 35562 SRR32880278 SRX28160879 SRS24513817 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 5 GSM8875048   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 5 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875048 GSM8875048: 3dpa blastema unexercised control bio rep 5; Danio rerio; RNA Seq GSM8875048 r1 GSM8875048 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_5_raw.fastq.gz fastq 3076092628.0 25213874.0 GSM8875048 r1 0:122 A:850913805;C:643783202;G:725071885;T:856245838;N:77898 122       850913805 643783202 725071885 856245838 77898 SRX28160879 SRS24513817 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35563 35563 SRR32880279 SRX28160878 SRS24513816 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 4 GSM8875047   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 4 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875047 GSM8875047: 3dpa blastema unexercised control bio rep 4; Danio rerio; RNA Seq GSM8875047 r1 GSM8875047 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_4_raw.fastq.gz fastq 3458014848.0 28344384.0 GSM8875047 r1 0:122 A:946385067;C:748704825;G:821787294;T:941050744;N:86918 122       946385067 748704825 821787294 941050744 86918 SRX28160878 SRS24513816 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35564 35564 SRR32880280 SRX28160877 SRS24513815 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 3 GSM8875046   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 3 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875046 GSM8875046: 3dpa blastema unexercised control bio rep 3; Danio rerio; RNA Seq GSM8875046 r1 GSM8875046 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_3_raw.fastq.gz fastq 3750141896.0 30738868.0 GSM8875046 r1 0:122 A:1016915650;C:830734179;G:908080650;T:994316527;N:94890 122       1016915650 830734179 908080650 994316527 94890 SRX28160877 SRS24513815 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35565 35565 SRR32880281 SRX28160876 SRS24513814 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 2 GSM8875045   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 2 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875045 GSM8875045: 3dpa blastema unexercised control bio rep 2; Danio rerio; RNA Seq GSM8875045 r1 GSM8875045 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_2_raw.fastq.gz fastq 3559797740.0 29178670.0 GSM8875045 r1 0:122 A:940502236;C:815297194;G:877321806;T:926584991;N:91513 122       940502236 815297194 877321806 926584991 91513 SRX28160876 SRS24513814 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35566 35566 SRR32880282 SRX28160875 SRS24513812 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 1 GSM8875044   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 1 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875044 GSM8875044: 3dpa blastema unexercised control bio rep 1; Danio rerio; RNA Seq GSM8875044 r1 GSM8875044 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_1_raw.fastq.gz fastq 3410581248.0 27955584.0 GSM8875044 r1 0:122 A:908666390;C:784237057;G:832115119;T:885476069;N:86613 122       908666390 784237057 832115119 885476069 86613 SRX28160875 SRS24513812 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
36272 36272 SRR298567 SRX079845 SRS212651 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   ZiliIPTes GSM727524   tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL ZiliIPTes three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. RNA obtained from immunoprecipitation with Zili antibody   Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727524 GSM727524: ZiliIPTes GSM727524: ZiliIPTes GSM727524: ZiliIPTes 1   GEO Accession:GSM727524 RNA-Seq TRANSCRIPTOMIC size fractionation 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> SRP007331   read name barcode proc directive:ignore ZiliIPTes.fastq fastq 995759064.0 27659974.0 GSM727524 1 0:36   36                 SRX079845 SRS212651 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0537   0.03117   0.95856   0.42091   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Trunk Surface Structure
36335 36335 SRR398322 SRX115580 SRS285697 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   miRNA GFP minus GSM861784   source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types miRNA GFP minus The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. whole zebrafish embryos at 24 hpf Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types GSM861784 GSM861784: miRNA GFP minus; Danio rerio; RNA Seq GSM861784 1 GSM861784: miRNA GFP minus 1   GEO Accession:GSM861784 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <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> SRP010291     miRNA_CNTL_WT.fastq.gz fastq 295021332.0 8195037.0 GSM861784 r1 0:36 A:70414178;C:53495749;G:76994313;T:87833261;N:6283831 36       70414178 53495749 76994313 87833261 6283831 SRX115580 SRS285697 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.02832   0.02716   0.99957   0.43137   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Trunk Surface Structure
36385 36385 SRR516135 SRX156099 SRS346038 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr31 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr31 5m 1 zebrafish Nr31 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         1482677008.0 19508908.0 zebrafish Nr31 5m 1 1 0:76 A:385413939;C:354317020;G:354043481;T:388361606;N:540962 76       385413939 354317020 354043481 388361606 540962 SRX156099 SRS346038 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9273   0.08335   0.67898   0.48956   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36386 36386 SRR516140 SRX156099 SRS346038 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr31 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr31 5m 1 zebrafish Nr31 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         388560032.0 5112632.0 zebrafish Nr31 5m 1 2 0:76 A:102207965;C:91473514;G:92119606;T:102551859;N:207088 76       102207965 91473514 92119606 102551859 207088 SRX156099 SRS346038 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92486   0.08531   0.67663   0.49425   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36387 36387 SRR516134 SRX156098 SRS346037 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr30 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr30 5m 1 zebrafish Nr30 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         1675582184.0 22047134.0 zebrafish Nr30 5m 1 1 0:76 A:458929887;C:381230210;G:376734439;T:457916852;N:770796 76       458929887 381230210 376734439 457916852 770796 SRX156098 SRS346037 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91832   0.10303   0.71455   0.49444   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36388 36388 SRR516139 SRX156098 SRS346037 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr30 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr30 5m 1 zebrafish Nr30 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         477065908.0 6277183.0 zebrafish Nr30 5m 1 2 0:76 A:131927852;C:107181234;G:106214626;T:131489254;N:252942 76       131927852 107181234 106214626 131489254 252942 SRX156098 SRS346037 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91581   0.10754   0.71577   0.49994   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36389 36389 SRR516133 SRX156097 SRS346036 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr29 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr29 5m 1 zebrafish Nr29 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         1305047832.0 17171682.0 zebrafish Nr29 5m 1 1 0:76 A:362467093;C:292043132;G:289641844;T:360441501;N:454262 76       362467093 292043132 289641844 360441501 454262 SRX156097 SRS346036 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90448   0.11905   0.70246   0.47656   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36390 36390 SRR516138 SRX156097 SRS346036 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr29 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr29 5m 1 zebrafish Nr29 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931     110307_DanioRerio_Nr29_5m_w1_s_1.fq fastq 457287972.0 6016947.0 zebrafish Nr29 5m 1 2 0:76 A:128212070;C:101000378;G:100136000;T:127695086;N:244438 76       128212070 101000378 100136000 127695086 244438 SRX156097 SRS346036 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90327   0.12466   0.70195   0.49568   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36391 36391 SRR516132 SRX156096 SRS346035 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr28 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr28 5m 1 zebrafish Nr28 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931     110104_DanioRerio_Nr28_5m_l5.fq fastq 778479248.0 10243148.0 zebrafish Nr28 5m 1 1 0:76 A:207103962;C:183338330;G:183353815;T:204420105;N:263036 76       207103962 183338330 183353815 204420105 263036 SRX156096 SRS346035 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91711   0.08403   0.72218   0.46568   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36392 36392 SRR516137 SRX156096 SRS346035 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr28 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr28 5m 1 zebrafish Nr28 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931     110307_DanioRerio_Nr28_5m_w1_s_2.fq fastq 1004119144.0 13212094.0 zebrafish Nr28 5m 1 2 0:76 A:269579079;C:233472158;G:233160786;T:267709479;N:197642 76       269579079 233472158 233160786 267709479 197642 SRX156096 SRS346035 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92125   0.09157   0.72056   0.4782   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36393 36393 SRR516131 SRX156095 SRS346034 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr27 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr27 5m 1 zebrafish Nr27 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         1689987528.0 22236678.0 zebrafish Nr27 5m 1 1 0:76 A:462852366;C:385867681;G:380635625;T:460044585;N:587271 76       462852366 385867681 380635625 460044585 587271 SRX156095 SRS346034 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91288   0.1015   0.71293   0.488   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36394 36394 SRR516136 SRX156095 SRS346034 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr27 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr27 5m 1 zebrafish Nr27 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         421535824.0 5546524.0 zebrafish Nr27 5m 1 2 0:76 A:116434305;C:94958671;G:93876467;T:116039545;N:226836 76       116434305 94958671 93876467 116039545 226836 SRX156095 SRS346034 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90776   0.10459   0.71399   0.49081   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36395 36395 SRR516130 SRX156094 SRS346033 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr26 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr26 5m 1 zebrafish Nr26 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         1633478944.0 21493144.0 zebrafish Nr26 5m 1 1 0:76 A:435251153;C:384938751;G:380973255;T:432171855;N:143930 76       435251153 384938751 380973255 432171855 143930 SRX156094 SRS346033 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92486   0.08081   0.71969   0.50656   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36396 36396 SRR516129 SRX156093 SRS346032 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr25 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr25 5m 1 zebrafish Nr25 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931     101021_DanioRerio_Nr25_5m_l7.fq fastq 1893537644.0 24914969.0 zebrafish Nr25 5m 1 1 0:76 A:516246577;C:431589332;G:431233057;T:514385629;N:83049 76       516246577 431589332 431233057 514385629 83049 SRX156093 SRS346032 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89513   0.11188   0.70591   0.47827   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36397 36397 SRR516128 SRX156092 SRS346031 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr23 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr23 5m 1 zebrafish Nr23 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931     101021_DanioRerio_Nr23_5m_l6.fq fastq 2271040360.0 29882110.0 zebrafish Nr23 5m 1 1 0:76 A:602084142;C:529733757;G:524301688;T:614827528;N:93245 76       602084142 529733757 524301688 614827528 93245 SRX156092 SRS346031 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92194   0.09655   0.70463   0.47059   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36398 36398 SRR516127 SRX156091 SRS346030 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr22 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr22 5m 1 zebrafish Nr22 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2812847324.0 37011149.0 zebrafish Nr22 5m 1 1 0:76 A:760320146;C:645617435;G:643672544;T:763112485;N:124714 76       760320146 645617435 643672544 763112485 124714 SRX156091 SRS346030 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93272   0.08997   0.70755   0.52272   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36399 36399 SRR516126 SRX156090 SRS346029 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr21 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr21 5m 1 zebrafish Nr21 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2331404728.0 30676378.0 zebrafish Nr21 5m 1 1 0:76 A:630276643;C:539444103;G:529126097;T:632442560;N:115325 76       630276643 539444103 529126097 632442560 115325 SRX156090 SRS346029 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92747   0.10341   0.70414   0.49626   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36400 36400 SRR516125 SRX156089 SRS346028 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr18 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr18 3.5y 1 zebrafish Nr18 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2653618888.0 34916038.0 zebrafish Nr18 3.5y 1 1 0:76 A:728660211;C:598216653;G:601771842;T:724871715;N:98467 76       728660211 598216653 601771842 724871715 98467 SRX156089 SRS346028 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91227   0.10895   0.71802   0.49946   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36401 36401 SRR516124 SRX156088 SRS346027 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr14 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr14 3.5y 1 zebrafish Nr14 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2013201012.0 26489487.0 zebrafish Nr14 3.5y 1 1 0:76 A:554778161;C:456082219;G:445029202;T:557232699;N:78731 76       554778161 456082219 445029202 557232699 78731 SRX156088 SRS346027 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90845   0.1164   0.71236   0.48939   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36402 36402 SRR516123 SRX156087 SRS346026 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr13 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr13 3.5y 1 zebrafish Nr13 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2680273532.0 35266757.0 zebrafish Nr13 3.5y 1 1 0:76 A:740111520;C:588329849;G:606909161;T:744802954;N:120048 76       740111520 588329849 606909161 744802954 120048 SRX156087 SRS346026 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.85899   0.11949   0.71595   0.48655   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36403 36403 SRR516122 SRX156086 SRS346025 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr12 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr12 3.5y 1 zebrafish Nr12 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2982635200.0 39245200.0 zebrafish Nr12 3.5y 1 1 0:76 A:829678392;C:650275344;G:659157904;T:842323646;N:1199914 76       829678392 650275344 659157904 842323646 1199914 SRX156086 SRS346025 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88932   0.12521   0.71638   0.53514   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36404 36404 SRR516121 SRX156085 SRS346024 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr11 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr11 3.5y 1 zebrafish Nr11 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</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> SRP013931         2696915708.0 35485733.0 zebrafish Nr11 3.5y 1 1 0:76 A:749305835;C:599264137;G:607414252;T:740194221;N:737263 76       749305835 599264137 607414252 740194221 737263 SRX156085 SRS346024 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.86902   0.11557   0.71461   0.49255   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36617 36617 SRR941753 SRX326770 SRS463196 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 2 Pos2   strain:EK|isolate:4|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 2 Pectoral Posterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other 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> SRP027598     Pos_R2.fastq fastq 2119489050.0 42389781.0 Pos R2 0:50 A:551122430;C:507870866;G:499494183;T:555469321;N:5532250 50       551122430 507870866 499494183 555469321 5532250 SRX326770 SRS463196 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.90238   0.08924   0.71303   0.43405   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36618 36618 SRR941754 SRX326769 SRS463195 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 1 Pos1   strain:EK|isolate:3|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 1 Pectoral Fin Posterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other 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> SRP027598         1839141950.0 36782839.0 Pos R1 0:50 A:461313296;C:455413049;G:451484067;T:466101993;N:4829545 50       461313296 455413049 451484067 466101993 4829545 SRX326769 SRS463195 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.91205   0.06923   0.71656   0.42651   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36619 36619 SRR941751 SRX326756 SRS463187 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 2 Ant2   strain:EK|isolate:2|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 2 Pectoral Fin Anterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other 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> SRP027598     Ant_R2.fastq fastq 2146396250.0 42927925.0 Ant R2 0:50 A:562140204;C:509390346;G:501995610;T:567232459;N:5637631 50       562140204 509390346 501995610 567232459 5637631 SRX326756 SRS463187 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89956   0.09279   0.70997   0.44847   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36620 36620 SRR941749 SRX326754 SRS463185 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 1 Ant1   strain:EK|isolate:1|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 1 Pectoral Fin Anterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other 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> SRP027598     Ant_R1.fastq fastq 2178096950.0 43561939.0 Ant R1 0:50 A:568580441;C:517705965;G:509551928;T:576519788;N:5738828 50       568580441 517705965 509551928 576519788 5738828 SRX326754 SRS463185 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89833   0.08959   0.71494   0.44088   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36712 36712 SRR835167 SRX271963 SRS416259 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 116h 53 GSM1129625   tissue:melanocytes|hpf dm 116h 53 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129625 GSM1129625: dm 116h 53; Danio rerio; RNA Seq GSM1129625 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129625 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_116h_53_440.fq.bz2 fastq 203842506.0 4853393.0 GSM1129625 r1 0:42 A:49784918;C:48871504;G:45835011;T:59338271;N:12802 42       49784918 48871504 45835011 59338271 12802 SRX271963 SRS416259 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.82741   0.14973   0.84893   0.53644   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36713 36713 SRR835166 SRX271962 SRS416258 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 97h 41 440 GSM1129624   tissue:melanocytes|hpf dm 97h 41 440 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129624 GSM1129624: dm 97h 41 440; Danio rerio; RNA Seq GSM1129624 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129624 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_97h_41_440.fq.bz2 fastq 199638768.0 4753304.0 GSM1129624 r1 0:42 A:45958194;C:50367228;G:48451580;T:54849238;N:12528 42       45958194 50367228 48451580 54849238 12528 SRX271962 SRS416258 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.85741   0.09897   0.84112   0.53299   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36714 36714 SRR835165 SRX271961 SRS416257 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h FM 351 GSM1129623   tissue:melanocytes|hpf dm 77h FM 351 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129623 GSM1129623: dm 77h FM 351; Danio rerio; RNA Seq GSM1129623 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129623 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_FM_351_ATT.fq.bz2 fastq 194385384.0 5399594.0 GSM1129623 r1 0:36 A:45805148;C:47931006;G:41165284;T:59482433;N:1513 36       45805148 47931006 41165284 59482433 1513 SRX271961 SRS416257 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.77748   0.07764   0.87687   0.51575   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36715 36715 SRR835164 SRX271960 SRS416256 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 52 440 GSM1129622   tissue:melanocytes|hpf dm 77h 52 440 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129622 GSM1129622: dm 77h 52 440; Danio rerio; RNA Seq GSM1129622 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129622 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_52_440.fq.bz2 fastq 105047586.0 2501133.0 GSM1129622 r1 0:42 A:24711000;C:26459041;G:24869198;T:29001957;N:6390 42       24711000 26459041 24869198 29001957 6390 SRX271960 SRS416256 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.88862   0.09219   0.83611   0.55476   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36716 36716 SRR835163 SRX271959 SRS416255 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 43 440 GSM1129621   tissue:melanocytes|hpf dm 77h 43 440 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129621 GSM1129621: dm 77h 43 440; Danio rerio; RNA Seq GSM1129621 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129621 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_43_440.fq.bz2 fastq 371553084.0 8846502.0 GSM1129621 r1 0:42 A:84994407;C:91269417;G:87188701;T:108077735;N:22824 42       84994407 91269417 87188701 108077735 22824 SRX271959 SRS416255 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.86495   0.09748   0.83684   0.52833   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36719 36719 SRR835160 SRX271956 SRS416252 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 28 436 GSM1129618   tissue:melanocytes|hpf dm 77h 28 436 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129618 GSM1129618: dm 77h 28 436; Danio rerio; RNA Seq GSM1129618 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129618 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_28_436_CACT.fq.bz2 fastq 214752678.0 5113159.0 GSM1129618 r1 0:42 A:50210098;C:62230664;G:49216487;T:52926929;N:168500 42       50210098 62230664 49216487 52926929 168500 SRX271956 SRS416252 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.80956   0.02412   0.87024   0.62475   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36720 36720 SRR835159 SRX271955 SRS416251 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 28 351 GSM1129617   tissue:melanocytes|hpf dm 77h 28 351 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129617 GSM1129617: dm 77h 28 351; Danio rerio; RNA Seq GSM1129617 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129617 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_28_351_CACT.fq.bz2 fastq 84584556.0 2349571.0 GSM1129617 r1 0:36 A:19843286;C:24761303;G:18855233;T:21124051;N:683 36       19843286 24761303 18855233 21124051 683 SRX271955 SRS416251 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75246   0.02663   0.87054   0.59024   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36721 36721 SRR835158 SRX271954 SRS416250 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 27 436 GSM1129616   tissue:melanocytes|hpf dm 77h 27 436 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129616 GSM1129616: dm 77h 27 436; Danio rerio; RNA Seq GSM1129616 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129616 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_27_436_TTAT.fq.bz2 fastq 194114466.0 4621773.0 GSM1129616 r1 0:42 A:44579558;C:47759429;G:44539735;T:57080409;N:155335 42       44579558 47759429 44539735 57080409 155335 SRX271954 SRS416250 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.80787   0.04019   0.86263   0.57373   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36722 36722 SRR835157 SRX271953 SRS416249 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 27 351 GSM1129615   tissue:melanocytes|hpf dm 77h 27 351 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129615 GSM1129615: dm 77h 27 351; Danio rerio; RNA Seq GSM1129615 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129615 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_27_351_TTAT.fq.bz2 fastq 113087304.0 3141314.0 GSM1129615 r1 0:36 A:26171623;C:27323878;G:24871328;T:34719586;N:889 36       26171623 27323878 24871328 34719586 889 SRX271953 SRS416249 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75375   0.04337   0.85878   0.5311   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36723 36723 SRR835156 SRX271952 SRS416248 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 26 433 GSM1129614   tissue:melanocytes|hpf dm 77h 26 433 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129614 GSM1129614: dm 77h 26 433; Danio rerio; RNA Seq GSM1129614 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129614 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_26_433_AGAT.fq.bz2 fastq 34005804.0 809662.0 GSM1129614 r1 0:42 A:8766789;C:8066807;G:8338043;T:8833768;N:397 42       8766789 8066807 8338043 8833768 397 SRX271952 SRS416248 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.81802   0.05684   0.88787   0.56756   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36724 36724 SRR835155 SRX271951 SRS416247 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 26 351 GSM1129613   tissue:melanocytes|hpf dm 77h 26 351 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129613 GSM1129613: dm 77h 26 351; Danio rerio; RNA Seq GSM1129613 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129613 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_26_351_AGAT.fq.bz2 fastq 101340432.0 2815012.0 GSM1129613 r1 0:36 A:26592120;C:23518331;G:24503636;T:26725495;N:850 36       26592120 23518331 24503636 26725495 850 SRX271951 SRS416247 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75158   0.05787   0.88986   0.57167   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36727 36727 SRR835152 SRX271948 SRS416244 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 25 433 GSM1129610   tissue:melanocytes|hpf dm 77h 25 433 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129610 GSM1129610: dm 77h 25 433; Danio rerio; RNA Seq GSM1129610 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129610 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_25_433_TCTT.fq.bz2 fastq 489386604.0 11652062.0 GSM1129610 r1 0:42 A:99597908;C:134563195;G:119005661;T:136214210;N:5630 42       99597908 134563195 119005661 136214210 5630 SRX271948 SRS416244 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.79072   0.08396   0.87497   0.51318   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure

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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");;