{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[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.", null, null, "Zebrafish rods expressing ES1 and EGFP", "ES1 3", "SAMD00044057", null, "sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044057", "DRX045209", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "1050Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044057", null, null, null, 371748120.0, 3469843.0, "DRR050167", "0:107.14", "A:107190409;C:79475572;G:83520360;T:101561779;N:0", 107, null, null, null, 107190409, 79475572, 83520360, 101561779, 0, "DRX045209", "DRS025834", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.81026, null, 0.26715, null, 0.86953, null, 0.52321, null, 51, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, "Zebrafish rods expressing ES1 and EGFP", "ES1 2", "SAMD00044056", null, "sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044056", "DRX045208", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "1280Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044056", null, null, null, 425549011.0, 3275261.0, "DRR050166", "0:129.93", "A:126640704;C:86415371;G:90822163;T:121670773;N:0", 129, null, null, null, 126640704, 86415371, 90822163, 121670773, 0, "DRX045208", "DRS025833", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.80223, null, 0.31429, null, 0.85861, null, 0.5272, null, 57, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, "Zebrafish rods expressing ES1 and EGFP", "ES1 1", "SAMD00044055", null, "sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044055", "DRX045207", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "1470Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044055", null, null, null, 584599765.0, 3941083.0, "DRR050165", "0:148.33", "A:164329030;C:129885620;G:136727379;T:153657736;N:0", 148, null, null, null, 164329030, 129885620, 136727379, 153657736, 0, "DRX045207", "DRS025832", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.83769, null, 0.25395, null, 0.83116, null, 0.52784, null, 185, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, "Zebrafish rods expressing EGFP", "EGFP 3", "SAMD00044054", null, "sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044054", "DRX045206", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "880Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044054", null, null, null, 343014114.0, 3827762.0, "DRR050164", "0:89.61", "A:99421434;C:73070267;G:77738821;T:92783592;N:0", 89, null, null, null, 99421434, 73070267, 77738821, 92783592, 0, "DRX045206", "DRS025831", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.78953, null, 0.25529, null, 0.87367, null, 0.52148, null, 24, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, "Zebrafish rods expressing EGFP", "EGFP 2", "SAMD00044053", null, "sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044053", "DRX045205", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "1370Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044053", null, null, null, 533069427.0, 3824140.0, "DRR050163", "0:139.40", "A:152608173;C:113928273;G:120051739;T:146481242;N:0", 139, null, null, null, 152608173, 113928273, 120051739, 146481242, 0, "DRX045205", "DRS025830", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.80412, null, 0.26768, null, 0.85338, null, 0.52255, null, 245, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, "Zebrafish rods expressing EGFP", "EGFP 1", "SAMD00044052", null, "sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00044052", "DRX045204", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "1130Application ReadForward1", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044052", null, null, null, 478262965.0, 4224064.0, "DRR050162", "0:113.22", "A:136348264;C:104872341;G:113114502;T:123927858;N:0", 113, null, null, null, 136348264, 104872341, 113114502, 123927858, 0, "DRX045204", "DRS025829", "DRA004229", "OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.", "Osaka university", 1, 0.86947, null, 0.29839, null, 0.83317, null, 0.51453, null, 80, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2016-03-09", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [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.", null, null, null, "Whole body of EMX3 / larval zebrafish 5dpf 3", "SAMD00182222", null, "sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182222", "DRX179844", "Emx3 / Larva body 3", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182222", null, null, null, 1759409208.0, 48872478.0, "DRR189379", "0:36", "A:401147348;C:424523813;G:426350919;T:507310828;N:76300", 36, null, null, null, 401147348, 424523813, 426350919, 507310828, 76300, "DRX179844", "DRS200410", "DRA008857", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.90975, null, 0.11439, null, 0.66076, null, 0.47775, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, "Whole body of EMX3 / larval zebrafish 5dpf 2", "SAMD00182221", null, "sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182221", "DRX179843", "Emx3 / Larva body 2", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182221", null, null, null, 1318201020.0, 36616695.0, "DRR189378", "0:36", "A:297850068;C:316786585;G:323717530;T:379789606;N:57231", 36, null, null, null, 297850068, 316786585, 323717530, 379789606, 57231, "DRX179843", "DRS200409", "DRA008857", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.9116, null, 0.11269, null, 0.65837, null, 0.46733, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, "Whole body of EMX3 / larval zebrafish 5dpf 1", "SAMD00182220", null, "sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182220", "DRX179842", "Emx3 / Larva body 1", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182220", null, null, null, 812483964.0, 22568999.0, "DRR189377", "0:36", "A:185173338;C:197790160;G:197482964;T:232000884;N:36618", 36, null, null, null, 185173338, 197790160, 197482964, 232000884, 36618, "DRX179842", "DRS200408", "DRA008857", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.91107, null, 0.1171, null, 0.65981, null, 0.47458, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, "Whole body of wild type larval zebrafish 5dpf 3", "SAMD00182219", null, "sample name:WT Larva body 3|genotype:wild type|tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182219", "DRX179841", "WT Larva body 3", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182219", null, null, null, 4030038144.0, 111945504.0, "DRR189376", "0:36", "A:943709984;C:971756680;G:977594500;T:1136798448;N:178532", 36, null, null, null, 943709984, 971756680, 977594500, 1136798448, 178532, "DRX179841", "DRS200449", "DRA008856", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.89574, null, 0.12331, null, 0.65831, null, 0.48096, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, "Whole body of wild type larval zebrafish 5dpf 2", "SAMD00182218", null, "sample name:WT Larva body 2|genotype:wild type|tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182218", "DRX179840", "WT Larva body 2", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182218", null, null, null, 1991670804.0, 55324189.0, "DRR189375", "0:36", "A:454367176;C:479012055;G:488407231;T:569793674;N:90668", 36, null, null, null, 454367176, 479012055, 488407231, 569793674, 90668, "DRX179840", "DRS200448", "DRA008856", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.90911, null, 0.12455, null, 0.65494, null, 0.47971, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, "Whole body of wild type larval zebrafish 5dpf 1", "SAMD00182217", null, "sample name:WT Larva body 1|genotype:wild type|tissue:whole body", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing of SAMD00182217", "DRX179839", "WT Larva body 1", "1", "SureSelect Strand Specific RNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", "360Application ReadForward1", "DRP003977", "Illumina HiSeq 3000 sequencing of SAMD00182217", null, null, null, 1018340100.0, 28287225.0, "DRR189374", "0:36", "A:233370050;C:244140659;G:247795084;T:292989542;N:44765", 36, null, null, null, 233370050, 244140659, 247795084, 292989542, 44765, "DRX179839", "DRS200447", "DRA008856", "NIG|National Institute of Genetics (Japan)", "National Institute of Genetics (Japan)", 1, 0.91078, null, 0.12578, null, 0.6524, null, 0.48016, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2021-08-08", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, "The remaining part of body of control fish 7dpf", "Control body", "SAMD00065411", null, "sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065411", "DRX069311", "Control body", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "360Application ReadForward1", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065411", null, null, null, 2653100352.0, 73697232.0, "DRR075397", "0:36", "A:656791658;C:620507513;G:625038612;T:750671135;N:91434", 36, null, null, null, 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, null, 0.15749, null, 0.67048, null, 0.47755, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, "Biological replicate 2", "Fin xanthophore 03", "SAMD00172019", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172019", "DRX170142", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2320Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172019", null, null, null, 376558775.0, 1624500.0, "DRR179616", "0:231.80", "A:107837072;C:79508449;G:79372899;T:109840355;N:0", 231, null, null, null, 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, null, 0.10951, null, 0.90425, null, 0.59385, null, 311, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "Biological replicate 1", "Fin xanthophore 02", "SAMD00172018", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172018", "DRX170141", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2430Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172018", null, null, null, 515115515.0, 2124170.0, "DRR179615", "0:242.50", "A:138421982;C:119032803;G:119412227;T:138248503;N:0", 242, null, null, null, 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, null, 0.05858, null, 0.88051, null, 0.50917, null, 284, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "Biological replicate 1", "Fin xanthophore 01", "SAMD00172017", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172017", "DRX170140", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2470Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172017", null, null, null, 371242152.0, 1504407.0, "DRR179614", "0:246.77", "A:99341086;C:86126839;G:86264882;T:99509345;N:0", 246, null, null, null, 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, null, 0.06422, null, 0.85679, null, 0.5066, null, 56, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "Biological replicate 2", "Fin melanophore 03", "SAMD00172016", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172016", "DRX170139", "Zebrafish fin melanophore 03", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2480Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172016", null, null, null, 342802993.0, 1585538.0, "DRR179613", "0:216.21", "A:90833658;C:80789744;G:80463233;T:90716358;N:0", 216, null, null, null, 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, null, 0.03528, null, 0.88605, null, 0.47299, null, 285, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "Biological replicate 1", "Fin melanophore 02", "SAMD00172015", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172015", "DRX170138", "Zebrafish fin melanophore 02", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2160Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172015", null, null, null, 538412675.0, 2168231.0, "DRR179612", "0:248.32", "A:147128403;C:121854818;G:121564109;T:147865345;N:0", 248, null, null, null, 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, null, 0.07081, null, 0.89286, null, 0.5935, null, 283, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "Biological replicate 1", "Fin melanophore 01", "SAMD00172014", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172014", "DRX170137", "Zebrafish fin melanophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "2150Application ReadForward1", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172014", null, null, null, 282446840.0, 1311431.0, "DRR179611", "0:215.37", "A:74927237;C:66575483;G:66161471;T:74782649;N:0", 215, null, null, null, 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, null, 0.0335, null, 0.89248, null, 0.58813, null, 274, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.10666, null, 0.73176, null, 0.50978, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.09315, null, 0.73464, null, 0.48744, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.08016, null, 0.72845, null, 0.47549, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.10726, null, 0.72585, null, 0.4913, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.09489, null, 0.73093, null, 0.48493, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.09666, null, 0.73501, null, 0.48749, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.1036, null, 0.72474, null, 0.48261, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.10892, null, 0.73277, null, 0.51067, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, null, 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, null, 0.13032, null, 0.73669, null, 0.50473, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 104994334, 102642310, 101303422, 126578362, 16217, "ERX4862324", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92322, null, 0.08481, null, 0.71997, null, 0.45351, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 152016801, 139221646, 139332264, 182506912, 23926, "ERX4862162", "ERS4959146", "ERA3206646", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90335, null, 0.1072, null, 0.71784, null, 0.48228, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 148729943, 136337224, 136545524, 178606078, 66633, "ERX4862146", "ERS4959146", "ERA3206631", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.9026, null, 0.10732, null, 0.71683, null, 0.47346, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 102630499, 100472291, 99193964, 123775368, 45220, "ERX4862323", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92245, null, 0.08463, null, 0.71877, null, 0.45377, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 106135147, 102194661, 100594136, 125630448, 17322, "ERX4862322", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91779, null, 0.08112, null, 0.7161, null, 0.4437, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 103644078, 99946940, 98381633, 122768121, 47612, "ERX4862321", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91867, null, 0.08097, null, 0.71388, null, 0.44882, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 117075718, 111922649, 112057835, 140651082, 18214, "ERX4862320", "ERS4959149", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91312, null, 0.08654, null, 0.71747, null, 0.46716, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 114367789, 109551764, 109678406, 137546387, 53630, "ERX4862319", "ERS4959149", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91412, null, 0.08674, null, 0.71632, null, 0.46601, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 116971308, 106056823, 107128214, 139968487, 17699, "ERX4862318", "ERS4959148", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90722, null, 0.1158, null, 0.72287, null, 0.46674, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 114396758, 103865119, 105005018, 136994559, 51133, "ERX4862317", "ERS4959148", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90759, null, 0.11359, null, 0.7208, null, 0.47232, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 123893447, 111981365, 116049412, 150953220, 20602, "ERX4862316", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90777, null, 0.11921, null, 0.7137, null, 0.48182, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 121063841, 109534722, 113610951, 147602721, 53899, "ERX4862315", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.907, null, 0.11935, null, 0.71364, null, 0.48543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [32541, "SRR29303120", "SRX24820197", "SRS21534299", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L6H 1 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L6H 1", "L6H 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 143411079, 162001488, 168382605, 146007422, 163861, "SRX24820197", "SRS21534299", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01303, null, 0.00337, null, 0.99472, null, 0.5628, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32542, "SRR29303121", "SRX24820196", "SRS21534298", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L3H 3 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L3H 3", "L3H 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 176614297, 190760467, 197157923, 173400138, 192878, "SRX24820196", "SRS21534298", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01163, null, 0.00356, null, 0.99379, null, 0.55469, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32543, "SRR29303122", "SRX24820195", "SRS21534297", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L3H 2 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L3H 2", "L3H 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 109695797, 132121151, 127787221, 119539033, 11619, "SRX24820195", "SRS21534297", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.05359, null, 0.01132, null, 0.98924, null, 0.55364, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32544, "SRR29303123", "SRX24820194", "SRS21534296", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L3H 1 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L3H 1", "L3H 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 130437158, 141969110, 146479841, 132605147, 10759, "SRX24820194", "SRS21534296", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.13403, null, 0.01834, null, 0.98735, null, 0.54849, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32545, "SRR29303124", "SRX24820193", "SRS21534295", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L1H 3 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L1H 3", "L1H 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 118598837, 136729611, 142993590, 126201873, 9916, "SRX24820193", "SRS21534295", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.00829, null, 0.00187, null, 0.99472, null, 0.54701, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32546, "SRR29303125", "SRX24820192", "SRS21534294", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L1H 2 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L1H 2", "L1H 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 126751483, 135818134, 141122995, 137953543, 51008, "SRX24820192", "SRS21534294", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.33438, null, 0.08101, null, 0.98238, null, 0.53337, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32547, "SRR29303126", "SRX24820191", "SRS21534293", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L1H 1 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L1H 1", "L1H 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 212568445, 243497911, 260145458, 213851032, 33436, "SRX24820191", "SRS21534293", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.64143, null, 0.02683, null, 0.98683, null, 0.5342, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32548, "SRR29303127", "SRX24820190", "SRS21534292", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 3 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 3", "DD 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 157267065, 168909886, 178336724, 162865168, 80546, "SRX24820190", "SRS21534292", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.19375, null, 0.03528, null, 0.98827, null, 0.55124, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32549, "SRR29303128", "SRX24820189", "SRS21534291", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L6H 3 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L6H 3", "L6H 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 126813056, 141881980, 147676363, 134665008, 144665, "SRX24820189", "SRS21534291", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.09301, null, 0.01507, null, 0.99042, null, 0.54323, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32550, "SRR29303129", "SRX24820188", "SRS21534290", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L6H 2 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L6H 2", "L6H 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 138521192, 148068464, 150615597, 134408189, 149190, "SRX24820188", "SRS21534290", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01523, null, 0.00336, null, 0.9933, null, 0.57685, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32551, "SRR29303130", "SRX24820187", "SRS21534289", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 2 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 2", "DD 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 162899595, 189209828, 187422113, 167222837, 186564, "SRX24820187", "SRS21534289", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.02266, null, 0.00566, null, 0.99334, null, 0.56959, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32552, "SRR29303131", "SRX24820186", "SRS21534288", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 1 miRNA", null, "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", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 1", "DD 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "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, null, null, null, 127336994, 143901414, 142437491, 126515166, 141797, "SRX24820186", "SRS21534288", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01404, null, 0.00313, null, 0.99484, null, 0.56573, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema exercised exp bio rep 5", "GSM8875053", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 1051289152, 808410920, 908646262, 1064964960, 94992, "SRX28160884", "SRS24513822", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema exercised exp bio rep 4", "GSM8875052", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 753716648, 572683669, 633777091, 756074187, 68889, "SRX28160883", "SRS24513821", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema exercised exp bio rep 3", "GSM8875051", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 929692130, 705713811, 773972336, 917030832, 85835, "SRX28160882", "SRS24513820", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema exercised exp bio rep 2", "GSM8875050", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 912008882, 704589377, 783108238, 920018852, 84605, "SRX28160881", "SRS24513819", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema exercised exp bio rep 1", "GSM8875049", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 1050863937, 775277972, 866627322, 1051571183, 95908, "SRX28160880", "SRS24513818", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema unexercised control bio rep 5", "GSM8875048", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 850913805, 643783202, 725071885, 856245838, 77898, "SRX28160879", "SRS24513817", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema unexercised control bio rep 4", "GSM8875047", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 946385067, 748704825, 821787294, 941050744, 86918, "SRX28160878", "SRS24513816", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema unexercised control bio rep 3", "GSM8875046", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 1016915650, 830734179, 908080650, 994316527, 94890, "SRX28160877", "SRS24513815", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema unexercised control bio rep 2", "GSM8875045", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 940502236, 815297194, 877321806, 926584991, 91513, "SRX28160876", "SRS24513814", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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\u2014applied during blastema establishment\u2014impairs 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", null, null, null, "3dpa blastema unexercised control bio rep 1", "GSM8875044", null, "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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP573530", null, null, "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, null, null, null, 908666390, 784237057, 832115119, 885476069, 86613, "SRX28160875", "SRS24513812", "SRA2100952", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-03-27", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, "pubmed:21743441", null, "ZiliIPTes", "GSM727524", null, "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", null, "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 \u00c2\u00b5l Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 \u00c2\u00b5l. 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.", null, "strain:TL", "GSM727524", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "1", null, "GEO Accession:GSM727524", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP007331", null, "read name barcode proc directive:ignore", "ZiliIPTes.fastq", "fastq", 995759064.0, 27659974.0, "GSM727524 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079845", "SRS212651", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.0537, null, 0.03117, null, 0.95856, null, 0.42091, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Trunk", "Surface Structure"], [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 \u201chyper angiogenesis\u201d 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.", null, "pubmed:22340502", null, "miRNA GFP minus", "GSM861784", null, "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.", null, "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", null, "GEO Accession:GSM861784", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "360Application ReadForward1", "SRP010291", null, null, "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, null, null, null, 70414178, 53495749, 76994313, 87833261, 6283831, "SRX115580", "SRS285697", "SRA049243", "GEO", "Nathan Lawson Lab, PGFE, Umass Medical School", 1, 0.02832, null, 0.02716, null, 0.99957, null, 0.43137, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-01-12", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr31 5m 1", "zebrafish Nr31 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 1482677008.0, 19508908.0, "zebrafish Nr31 5m 1 1", "0:76", "A:385413939;C:354317020;G:354043481;T:388361606;N:540962", 76, null, null, null, 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, null, 0.08335, null, 0.67898, null, 0.48956, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr31 5m 1", "zebrafish Nr31 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 388560032.0, 5112632.0, "zebrafish Nr31 5m 1 2", "0:76", "A:102207965;C:91473514;G:92119606;T:102551859;N:207088", 76, null, null, null, 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, null, 0.08531, null, 0.67663, null, 0.49425, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr30 5m 1", "zebrafish Nr30 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 1675582184.0, 22047134.0, "zebrafish Nr30 5m 1 1", "0:76", "A:458929887;C:381230210;G:376734439;T:457916852;N:770796", 76, null, null, null, 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, null, 0.10303, null, 0.71455, null, 0.49444, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr30 5m 1", "zebrafish Nr30 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 477065908.0, 6277183.0, "zebrafish Nr30 5m 1 2", "0:76", "A:131927852;C:107181234;G:106214626;T:131489254;N:252942", 76, null, null, null, 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, null, 0.10754, null, 0.71577, null, 0.49994, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr29 5m 1", "zebrafish Nr29 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 1305047832.0, 17171682.0, "zebrafish Nr29 5m 1 1", "0:76", "A:362467093;C:292043132;G:289641844;T:360441501;N:454262", 76, null, null, null, 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, null, 0.11905, null, 0.70246, null, 0.47656, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr29 5m 1", "zebrafish Nr29 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, "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, null, null, null, 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, null, 0.12466, null, 0.70195, null, 0.49568, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2013-03-11", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr28 5m 1", "zebrafish Nr28 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, "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, null, null, null, 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, null, 0.08403, null, 0.72218, null, 0.46568, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2013-03-11", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr28 5m 1", "zebrafish Nr28 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, "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, null, null, null, 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, null, 0.09157, null, 0.72056, null, 0.4782, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2013-03-11", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr27 5m 1", "zebrafish Nr27 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 1689987528.0, 22236678.0, "zebrafish Nr27 5m 1 1", "0:76", "A:462852366;C:385867681;G:380635625;T:460044585;N:587271", 76, null, null, null, 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, null, 0.1015, null, 0.71293, null, 0.488, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr27 5m 1", "zebrafish Nr27 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 421535824.0, 5546524.0, "zebrafish Nr27 5m 1 2", "0:76", "A:116434305;C:94958671;G:93876467;T:116039545;N:226836", 76, null, null, null, 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, null, 0.10459, null, 0.71399, null, 0.49081, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr26 5m 1", "zebrafish Nr26 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 1633478944.0, 21493144.0, "zebrafish Nr26 5m 1 1", "0:76", "A:435251153;C:384938751;G:380973255;T:432171855;N:143930", 76, null, null, null, 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, null, 0.08081, null, 0.71969, null, 0.50656, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr25 5m 1", "zebrafish Nr25 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, "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, null, null, null, 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, null, 0.11188, null, 0.70591, null, 0.47827, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr23 5m 1", "zebrafish Nr23 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, "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, null, null, null, 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, null, 0.09655, null, 0.70463, null, 0.47059, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2013-03-11", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr22 5m 1", "zebrafish Nr22 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2812847324.0, 37011149.0, "zebrafish Nr22 5m 1 1", "0:76", "A:760320146;C:645617435;G:643672544;T:763112485;N:124714", 76, null, null, null, 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, null, 0.08997, null, 0.70755, null, 0.52272, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr21 5m 1", "zebrafish Nr21 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2331404728.0, 30676378.0, "zebrafish Nr21 5m 1 1", "0:76", "A:630276643;C:539444103;G:529126097;T:632442560;N:115325", 76, null, null, null, 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, null, 0.10341, null, 0.70414, null, 0.49626, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr18 3.5y 1", "zebrafish Nr18 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2653618888.0, 34916038.0, "zebrafish Nr18 3.5y 1 1", "0:76", "A:728660211;C:598216653;G:601771842;T:724871715;N:98467", 76, null, null, null, 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, null, 0.10895, null, 0.71802, null, 0.49946, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr14 3.5y 1", "zebrafish Nr14 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2013201012.0, 26489487.0, "zebrafish Nr14 3.5y 1 1", "0:76", "A:554778161;C:456082219;G:445029202;T:557232699;N:78731", 76, null, null, null, 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, null, 0.1164, null, 0.71236, null, 0.48939, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr13 3.5y 1", "zebrafish Nr13 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2680273532.0, 35266757.0, "zebrafish Nr13 3.5y 1 1", "0:76", "A:740111520;C:588329849;G:606909161;T:744802954;N:120048", 76, null, null, null, 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, null, 0.11949, null, 0.71595, null, 0.48655, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr12 3.5y 1", "zebrafish Nr12 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2982635200.0, 39245200.0, "zebrafish Nr12 3.5y 1 1", "0:76", "A:829678392;C:650275344;G:659157904;T:842323646;N:1199914", 76, null, null, null, 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, null, 0.12521, null, 0.71638, null, 0.53514, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp", "zebrafish Nr11 3.5y 1", "zebrafish Nr11 1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "760Application ReadForward1", "SRP013931", null, null, null, null, 2696915708.0, 35485733.0, "zebrafish Nr11 3.5y 1 1", "0:76", "A:749305835;C:599264137;G:607414252;T:740194221;N:737263", 76, null, null, null, 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, null, 0.11557, null, 0.71461, null, 0.49255, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-06-26", "Adult", "Adult", "Skin", "Surface Structure"], [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.", null, null, "tissue comprising posterior most 2 fin rays", "Posterior pectoral fin replicate 2", "Pos2", null, "strain:EK|isolate:4|age:6 Month|sex:female", null, null, null, null, null, null, null, null, "RNA seq posterior pectoral fin replicate 2", "Pectoral Posterior 2", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP027598", null, null, "Pos_R2.fastq", "fastq", 2119489050.0, 42389781.0, "Pos R2", "0:50", "A:551122430;C:507870866;G:499494183;T:555469321;N:5532250", 50, null, null, null, 551122430, 507870866, 499494183, 555469321, 5532250, "SRX326770", "SRS463196", "SRA065677", "Duke Cell Biology|Poss", "Poss Lab, Duke Cell Biology", 1, 0.90238, null, 0.08924, null, 0.71303, null, 0.43405, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-07-19", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "tissue comprising posterior most 2 fin rays", "Posterior pectoral fin replicate 1", "Pos1", null, "strain:EK|isolate:3|age:6 Month|sex:female", null, null, null, null, null, null, null, null, "RNA seq posterior pectoral fin replicate 1", "Pectoral Fin Posterior 1", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP027598", null, null, null, null, 1839141950.0, 36782839.0, "Pos R1", "0:50", "A:461313296;C:455413049;G:451484067;T:466101993;N:4829545", 50, null, null, null, 461313296, 455413049, 451484067, 466101993, 4829545, "SRX326769", "SRS463195", "SRA065677", "Duke Cell Biology|Poss", "Poss Lab, Duke Cell Biology", 1, 0.91205, null, 0.06923, null, 0.71656, null, 0.42651, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-07-19", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "tissue comprising anterior most 2 fin rays", "Anterior pectoral fin replicate 2", "Ant2", null, "strain:EK|isolate:2|age:6 Month|sex:female", null, null, null, null, null, null, null, null, "RNA seq anterior pectoral fin replicate 2", "Pectoral Fin Anterior 2", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP027598", null, null, "Ant_R2.fastq", "fastq", 2146396250.0, 42927925.0, "Ant R2", "0:50", "A:562140204;C:509390346;G:501995610;T:567232459;N:5637631", 50, null, null, null, 562140204, 509390346, 501995610, 567232459, 5637631, "SRX326756", "SRS463187", "SRA065677", "Duke Cell Biology|Poss", "Poss Lab, Duke Cell Biology", 1, 0.89956, null, 0.09279, null, 0.70997, null, 0.44847, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-07-19", "Adult", "Adult", "Fin", "Surface Structure"], [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.", null, null, "tissue comprising anterior most 2 fin rays", "Anterior pectoral fin replicate 1", "Ant1", null, "strain:EK|isolate:1|age:6 Month|sex:female", null, null, null, null, null, null, null, null, "RNA seq anterior pectoral fin replicate 1", "Pectoral Fin Anterior 1", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP027598", null, null, "Ant_R1.fastq", "fastq", 2178096950.0, 43561939.0, "Ant R1", "0:50", "A:568580441;C:517705965;G:509551928;T:576519788;N:5738828", 50, null, null, null, 568580441, 517705965, 509551928, 576519788, 5738828, "SRX326754", "SRS463185", "SRA065677", "Duke Cell Biology|Poss", "Poss Lab, Duke Cell Biology", 1, 0.89833, null, 0.08959, null, 0.71494, null, 0.44088, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-07-19", "Adult", "Adult", "Fin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 116h 53", "GSM1129625", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129625", "GSM1129625: dm 116h 53; Danio rerio; RNA Seq", "GSM1129625 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129625", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 49784918, 48871504, 45835011, 59338271, 12802, "SRX271963", "SRS416259", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.82741, null, 0.14973, null, 0.84893, null, 0.53644, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 97h 41 440", "GSM1129624", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129624", "GSM1129624: dm 97h 41 440; Danio rerio; RNA Seq", "GSM1129624 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129624", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 45958194, 50367228, 48451580, 54849238, 12528, "SRX271962", "SRS416258", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.85741, null, 0.09897, null, 0.84112, null, 0.53299, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h FM 351", "GSM1129623", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129623", "GSM1129623: dm 77h FM 351; Danio rerio; RNA Seq", "GSM1129623 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129623", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 45805148, 47931006, 41165284, 59482433, 1513, "SRX271961", "SRS416257", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.77748, null, 0.07764, null, 0.87687, null, 0.51575, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 52 440", "GSM1129622", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129622", "GSM1129622: dm 77h 52 440; Danio rerio; RNA Seq", "GSM1129622 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129622", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 24711000, 26459041, 24869198, 29001957, 6390, "SRX271960", "SRS416256", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.88862, null, 0.09219, null, 0.83611, null, 0.55476, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 43 440", "GSM1129621", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129621", "GSM1129621: dm 77h 43 440; Danio rerio; RNA Seq", "GSM1129621 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129621", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 84994407, 91269417, 87188701, 108077735, 22824, "SRX271959", "SRS416255", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.86495, null, 0.09748, null, 0.83684, null, 0.52833, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 28 436", "GSM1129618", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129618", "GSM1129618: dm 77h 28 436; Danio rerio; RNA Seq", "GSM1129618 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129618", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 50210098, 62230664, 49216487, 52926929, 168500, "SRX271956", "SRS416252", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.80956, null, 0.02412, null, 0.87024, null, 0.62475, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 28 351", "GSM1129617", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129617", "GSM1129617: dm 77h 28 351; Danio rerio; RNA Seq", "GSM1129617 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129617", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 19843286, 24761303, 18855233, 21124051, 683, "SRX271955", "SRS416251", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.75246, null, 0.02663, null, 0.87054, null, 0.59024, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 27 436", "GSM1129616", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129616", "GSM1129616: dm 77h 27 436; Danio rerio; RNA Seq", "GSM1129616 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129616", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 44579558, 47759429, 44539735, 57080409, 155335, "SRX271954", "SRS416250", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.80787, null, 0.04019, null, 0.86263, null, 0.57373, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 27 351", "GSM1129615", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129615", "GSM1129615: dm 77h 27 351; Danio rerio; RNA Seq", "GSM1129615 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129615", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 26171623, 27323878, 24871328, 34719586, 889, "SRX271953", "SRS416249", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.75375, null, 0.04337, null, 0.85878, null, 0.5311, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 26 433", "GSM1129614", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129614", "GSM1129614: dm 77h 26 433; Danio rerio; RNA Seq", "GSM1129614 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129614", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 8766789, 8066807, 8338043, 8833768, 397, "SRX271952", "SRS416248", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.81802, null, 0.05684, null, 0.88787, null, 0.56756, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 26 351", "GSM1129613", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129613", "GSM1129613: dm 77h 26 351; Danio rerio; RNA Seq", "GSM1129613 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129613", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 26592120, 23518331, 24503636, 26725495, 850, "SRX271951", "SRS416247", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.75158, null, 0.05787, null, 0.88986, null, 0.57167, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:23874447", null, "dm 77h 25 433", "GSM1129610", null, "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", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129610", "GSM1129610: dm 77h 25 433; Danio rerio; RNA Seq", "GSM1129610 1", null, "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\u00b0C in mitfavc7. When held at 32\u00b0C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C 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\u00b0C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400\u00b5L 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 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R. Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C. Following centrifugation overlying Percoll was aspirated leaving the final 100\u00b5L containing the pigment cell pellet. Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS and kept on ice until mRNA extraction or FACS. FACS We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS. Following resuspension in 500\u00b5L cold DPBS with 2% FCS the enriched cell populations were screened through a 30uM cell filter Partec 04 0042 2316. Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz. Cells were illuminated using a 488 nm laser. Cells were gated on two attributes to separate cells from each other and from cellular debris. Cellular debris was detected using forward and side scatter selecting against the smallest particles 1\u00b5m or less. Cells were sorted based on detection using 510 530nm and 575 595nm filters corresponding to FL1 and FL2 in Figure 1D respectively. When excited by the 488 nm laser the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant. Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser and cluster at the lower left of the FACS plot. Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows. For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions. Following mRNA elution from the Dynabeads first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview. A universal primer sequence was also added to the three prime end of the first strand by template switching allowing for PCR amplification of the resultant cDNA [43 44]. Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa PCR cycle: 95C for 1 minute followed by 20 cycles of 98C for 25 seconds 60C for 1 minute 68C for 20 minutes cDNA was digested with AluI and RsaI restriction enzymes NEB. Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation. Since this reduced representation strategy might miss short cDNAs that lack both restriction sites we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers. This allows for the inclusion of short cDNAs in our libraries. Standard Illumina library preparations followed performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu. In brief a single A was added to the 3\u2019 end of each strand Y adapters ligated and library enrichment PCR performed followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length. Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45]. No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment. Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129610", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "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, null, null, null, 99597908, 134563195, 119005661, 136214210, 5630, "SRX271948", "SRS416244", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.79072, null, 0.08396, null, 0.87497, null, 0.51318, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Skin", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 476, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "unknown", "p2": "Surface Structure"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 389, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=ncRNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "WGS", "label": "WGS", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=WGS", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "cDNA", "label": "cDNA", "count": 329, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=cDNA", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 50, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=size+fractionation", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=RANDOM", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "DNase", "label": "DNase", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=DNase", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=PolyA", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "RT-PCR", "label": "RT-PCR", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=RT-PCR", "selected": false}, {"value": "PCR", "label": "PCR", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=PCR", "selected": false}, {"value": "other", "label": "other", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.library_selection=other", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=unknown&tissue_curation_coarse=Surface+Structure", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 429, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.platform=BGISEQ", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.platform=ION_TORRENT", "selected": false}, {"value": "ABI_SOLID", "label": "ABI_SOLID", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&experiment.platform=ABI_SOLID", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Adult", "label": "Adult", "count": 252, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Larval", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Juvenile", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Adult", "label": "Adult", "count": 242, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 95, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 71, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Undetermined", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Hatching", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Multi-stage", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Pharyngula", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Blastula", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&devstage_curation=Juvenile", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Skin", "label": "Skin", "count": 217, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&tissue_curation=Skin", "selected": false}, {"value": "Trunk", "label": "Trunk", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&tissue_curation=Trunk", "selected": false}, {"value": "Fin", "label": "Fin", "count": 104, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&tissue_curation=Fin", "selected": false}, {"value": "Scale", "label": "Scale", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&tissue_curation=Scale", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure", "results": [{"value": "unknown", "label": "unknown", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Surface+Structure", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": "36727", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation_coarse=Surface+Structure&_next=36727", "private": false, "allow_execute_sql": true, "query_ms": 134.59054198756348}