{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"ION_TORRENT\"", "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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044057", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044056", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044055", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044054", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044053", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP003043", "Ion Torrent PGM sequencing of SAMD00044052", 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"], [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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172019", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172018", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172017", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172016", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172015", 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172014", 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"], [5795, "ERR1698352", "ERX1767860", "ERS1417534", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 012 up 058 12", "SAMEA4518355", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518355|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 012 up 058 12 s", "IonXpressRNA 012 up 058 12 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_012_up_058_12.fastq.gz", "fastq", 2535299006.0, 33956077.0, "E MTAB 5173:IonXpressRNA 012 up 058 12", "0:74.66", "A:719061985;C:581906269;G:579932234;T:654398518;N:0", 74, null, null, null, 719061985, 581906269, 579932234, 654398518, 0, "ERX1767860", "ERS1417534", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.7343, null, 0.34119, null, 0.7359, null, 0.48406, null, 66, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5796, "ERR1698351", "ERX1767859", "ERS1417533", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 011 up 058 11", "SAMEA4518354", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518354|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 011 up 058 11|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 011 up 058 11|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 011 up 058 11 s", "IonXpressRNA 011 up 058 11 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_011_up_058_11.fastq.gz", "fastq", 3400774471.0, 38709756.0, "E MTAB 5173:IonXpressRNA 011 up 058 11", "0:87.85", "A:948991439;C:793389977;G:792539547;T:865853508;N:0", 87, null, null, null, 948991439, 793389977, 792539547, 865853508, 0, "ERX1767859", "ERS1417533", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.63968, null, 0.27033, null, 0.75213, null, 0.47966, null, 139, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5797, "ERR1698350", "ERX1767858", "ERS1417532", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 010 up 058 10", "SAMEA4518353", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518353|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 010 up 058 10|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 010 up 058 10|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 010 up 058 10 s", "IonXpressRNA 010 up 058 10 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_010_up_058_10.fastq.gz", "fastq", 3502667998.0, 39204781.0, "E MTAB 5173:IonXpressRNA 010 up 058 10", "0:89.34", "A:976977303;C:803330255;G:808731995;T:913628445;N:0", 89, null, null, null, 976977303, 803330255, 808731995, 913628445, 0, "ERX1767858", "ERS1417532", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.65846, null, 0.2815, null, 0.74028, null, 0.47784, null, 86, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5798, "ERR1698349", "ERX1767857", "ERS1417531", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 009 up 058 9", "SAMEA4518352", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518352|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 009 up 058 9|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 009 up 058 9|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 009 up 058 9 s", "IonXpressRNA 009 up 058 9 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_009_up_058_9.fastq.gz", "fastq", 3575088264.0, 39745481.0, "E MTAB 5173:IonXpressRNA 009 up 058 9", "0:89.95", "A:1011474126;C:809896078;G:807471974;T:946246086;N:0", 89, null, null, null, 1011474126, 809896078, 807471974, 946246086, 0, "ERX1767857", "ERS1417531", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.65266, null, 0.30274, null, 0.75286, null, 0.48527, null, 94, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5799, "ERR1698348", "ERX1767856", "ERS1417530", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 008 up 058 8", "SAMEA4518351", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518351|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 008 up 058 8|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 008 up 058 8|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 008 up 058 8 s", "IonXpressRNA 008 up 058 8 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_008_up_058_8.fastq.gz", "fastq", 3259710114.0, 38530802.0, "E MTAB 5173:IonXpressRNA 008 up 058 8", "0:84.60", "A:916053004;C:755694888;G:751125332;T:836836890;N:0", 84, null, null, null, 916053004, 755694888, 751125332, 836836890, 0, "ERX1767856", "ERS1417530", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.70995, null, 0.31365, null, 0.74781, null, 0.48846, null, 61, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5800, "ERR1698347", "ERX1767855", "ERS1417529", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 007 up 058 7", "SAMEA4518350", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518350|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 007 up 058 7|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 007 up 058 7|sex:male", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 007 up 058 7 s", "IonXpressRNA 007 up 058 7 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: male:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_007_up_058_7.fastq.gz", "fastq", 2307842164.0, 28984666.0, "E MTAB 5173:IonXpressRNA 007 up 058 7", "0:79.62", "A:634041732;C:548565089;G:545418985;T:579816358;N:0", 79, null, null, null, 634041732, 548565089, 545418985, 579816358, 0, "ERX1767855", "ERS1417529", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.67542, null, 0.2817, null, 0.74168, null, 0.47224, null, 37, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5801, "ERR1698346", "ERX1767854", "ERS1417528", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 006 up 058 6", "SAMEA4518349", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518349|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 006 up 058 6|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 006 up 058 6|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 006 up 058 6 s", "IonXpressRNA 006 up 058 6 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_006_up_058_6.fastq.gz", "fastq", 2239484857.0, 27021234.0, "E MTAB 5173:IonXpressRNA 006 up 058 6", "0:82.88", "A:637326624;C:506830056;G:503508207;T:591819970;N:0", 82, null, null, null, 637326624, 506830056, 503508207, 591819970, 0, "ERX1767854", "ERS1417528", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.66441, null, 0.31904, null, 0.74905, null, 0.47154, null, 122, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5802, "ERR1698345", "ERX1767853", "ERS1417527", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 005 up 058 5", "SAMEA4518348", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518348|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 005 up 058 5|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 005 up 058 5|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 005 up 058 5 s", "IonXpressRNA 005 up 058 5 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_005_up_058_5.fastq.gz", "fastq", 2920608487.0, 39573075.0, "E MTAB 5173:IonXpressRNA 005 up 058 5", "0:73.80", "A:814851327;C:678116994;G:691911192;T:735728974;N:0", 73, null, null, null, 814851327, 678116994, 691911192, 735728974, 0, "ERX1767853", "ERS1417527", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.60005, null, 0.25542, null, 0.76481, null, 0.4886, null, 12, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5803, "ERR1698344", "ERX1767852", "ERS1417526", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 004 up 058 4", "SAMEA4518347", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518347|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 004 up 058 4|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 004 up 058 4|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 004 up 058 4 s", "IonXpressRNA 004 up 058 4 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_004_up_058_4.fastq.gz", "fastq", 2989727396.0, 37953454.0, "E MTAB 5173:IonXpressRNA 004 up 058 4", "0:78.77", "A:802963810;C:722434772;G:742850530;T:721478284;N:0", 78, null, null, null, 802963810, 722434772, 742850530, 721478284, 0, "ERX1767852", "ERS1417526", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.76402, null, 0.32503, null, 0.74241, null, 0.4815, null, 128, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5804, "ERR1698343", "ERX1767851", "ERS1417525", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 003 up 058 3", "SAMEA4518346", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518346|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 003 up 058 3|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 003 up 058 3|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 003 up 058 3 s", "IonXpressRNA 003 up 058 3 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_003_up_058_3.fastq.gz", "fastq", 4068383115.0, 41996847.0, "E MTAB 5173:IonXpressRNA 003 up 058 3", "0:96.87", "A:1133167706;C:944306379;G:948626944;T:1042282086;N:0", 96, null, null, null, 1133167706, 944306379, 948626944, 1042282086, 0, "ERX1767851", "ERS1417525", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.54804, null, 0.22334, null, 0.76353, null, 0.49163, null, 93, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5805, "ERR1698342", "ERX1767850", "ERS1417524", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 002 up 058 2", "SAMEA4518345", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518345|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 002 up 058 2 s", "IonXpressRNA 002 up 058 2 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_002_up_058_2.fastq.gz", "fastq", 2679963893.0, 33552723.0, "E MTAB 5173:IonXpressRNA 002 up 058 2", "0:79.87", "A:709092431;C:635329399;G:670478210;T:665063853;N:0", 79, null, null, null, 709092431, 635329399, 670478210, 665063853, 0, "ERX1767850", "ERS1417524", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.43283, null, 0.18649, null, 0.81178, null, 0.52885, null, 116, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [5806, "ERR1698341", "ERX1767849", "ERS1417523", "ERP018188", "PRJEB16335", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol", "E-MTAB-5173", "Transcriptome Analysis", "17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173", null, "Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "IonXpressRNA 001 up 058 1", "SAMEA4518344", "School of Natural Science, Technology and Environmental Studies Sodertorn University", "ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518344|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 001 up 058 1|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 001 up 058 1|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "E MTAB 5173:IonXpressRNA 001 up 058 1 s", "IonXpressRNA 001 up 058 1 s", "RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 ethinylestradiol", "RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA", "Experimental Factor: female:sex|Experimental Factor: n1:compound", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 ethinylestradiol", "ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16", "IonXpressRNA_001_up_058_1.fastq.gz", "fastq", 3358902499.0, 39857024.0, "E MTAB 5173:IonXpressRNA 001 up 058 1", "0:84.27", "A:933405205;C:784111716;G:780404241;T:860981337;N:0", 84, null, null, null, 933405205, 784111716, 780404241, 860981337, 0, "ERX1767849", "ERS1417523", "ERA739176", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", "School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive", 1, 0.71789, null, 0.33159, null, 0.76619, null, 0.514, null, 56, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [15504, "ERR757154", "ERX701784", "ERS659467", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Normalization across length", "SAMEA3251321", "UNIVERSITY OF AMSTERDAM", "ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251321|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female X|common name:zebrafish|dev stage:Adult|sample name:Female X|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16", "RID0035_003.fastq.gz", "fastq", 275591336.0, 7611054.0, "ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2", "0:36.21", "A:72212971;C:63331647;G:68054270;T:71992448;N:0", 36, null, null, null, 72212971, 63331647, 68054270, 71992448, 0, "ERX701784", "ERS659467", "ERA410345", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.76262, null, 0.4273, null, 0.8101, null, 0.56676, null, 8, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2015-02-12", "Adult", "Adult", "Undetermined", "Undetermined"], [15505, "ERR757153", "ERX701783", "ERS659466", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Normalization across length", "SAMEA3251320", "UNIVERSITY OF AMSTERDAM", "ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251320|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female 002|common name:zebrafish|dev stage:Adult|sample name:Female 002|sex:female", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16", "RID0035_006.fastq.gz", "fastq", 193706106.0, 6343893.0, "ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1", "0:30.53", "A:52756888;C:42895374;G:46979869;T:51073975;N:0", 30, null, null, null, 52756888, 42895374, 46979869, 51073975, 0, "ERX701783", "ERS659466", "ERA410345", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74991, null, 0.41319, null, 0.83002, null, 0.55823, null, 8, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2015-02-12", "Adult", "Adult", "Undetermined", "Undetermined"], [15506, "ERR647638", "ERX604074", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_007.fastq.gz", "fastq", 181485343.0, 7581675.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7", "0:23.94", "A:49408107;C:35660562;G:44520624;T:51896050;N:0", 23, null, null, null, 49408107, 35660562, 44520624, 51896050, 0, "ERX604074", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75831, null, 0.16017, null, 0.90723, null, 0.48684, null, 13, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15507, "ERR647632", "ERX604068", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_001.fastq.gz", "fastq", 158714692.0, 5407747.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1", "0:29.35", "A:42098161;C:32991434;G:38596553;T:45028544;N:0", 29, null, null, null, 42098161, 32991434, 38596553, 45028544, 0, "ERX604068", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75901, null, 0.20293, null, 0.89505, null, 0.48215, null, 24, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15508, "ERR647636", "ERX604072", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_005.fastq.gz", "fastq", 124167412.0, 4838491.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5", "0:25.66", "A:33439510;C:24728035;G:30897675;T:35102192;N:0", 25, null, null, null, 33439510, 24728035, 30897675, 35102192, 0, "ERX604072", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.76027, null, 0.17783, null, 0.89692, null, 0.48421, null, 30, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15509, "ERR647635", "ERX604071", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_004.fastq.gz", "fastq", 124786630.0, 4701452.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4", "0:26.54", "A:33803418;C:24800330;G:30482560;T:35700322;N:0", 26, null, null, null, 33803418, 24800330, 30482560, 35700322, 0, "ERX604071", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74872, null, 0.18448, null, 0.89789, null, 0.50377, null, 12, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15510, "ERR647634", "ERX604070", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_003.fastq.gz", "fastq", 110526752.0, 4078127.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3", "0:27.10", "A:29453167;C:22981184;G:27444083;T:30648318;N:0", 27, null, null, null, 29453167, 22981184, 27444083, 30648318, 0, "ERX604070", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73961, null, 0.1804, null, 0.89686, null, 0.50069, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15511, "ERR647633", "ERX604069", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_002.fastq.gz", "fastq", 114721515.0, 4468497.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2", "0:25.67", "A:31387085;C:22123581;G:28270438;T:32940411;N:0", 25, null, null, null, 31387085, 22123581, 28270438, 32940411, 0, "ERX604069", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75767, null, 0.17199, null, 0.90118, null, 0.49949, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15512, "ERR647645", "ERX604081", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_014.fastq.gz", "fastq", 127742942.0, 5487454.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14", "0:23.28", "A:35700746;C:25577569;G:31187339;T:35277288;N:0", 23, null, null, null, 35700746, 25577569, 31187339, 35277288, 0, "ERX604081", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.72451, null, 0.1507, null, 0.91078, null, 0.47283, null, 30, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15513, "ERR647644", "ERX604080", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_013.fastq.gz", "fastq", 175319872.0, 7193103.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13", "0:24.37", "A:48008107;C:34657005;G:43047489;T:49607271;N:0", 24, null, null, null, 48008107, 34657005, 43047489, 49607271, 0, "ERX604080", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75539, null, 0.16288, null, 0.90388, null, 0.47538, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15514, "ERR647643", "ERX604079", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_012.fastq.gz", "fastq", 177443752.0, 7567733.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12", "0:23.45", "A:48143286;C:36300870;G:44060167;T:48939429;N:0", 23, null, null, null, 48143286, 36300870, 44060167, 48939429, 0, "ERX604079", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74839, null, 0.15018, null, 0.90782, null, 0.49076, null, 27, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15515, "ERR647642", "ERX604078", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_011.fastq.gz", "fastq", 163389373.0, 6320373.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11", "0:25.85", "A:44540588;C:32608476;G:40066295;T:46174014;N:0", 25, null, null, null, 44540588, 32608476, 40066295, 46174014, 0, "ERX604078", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75948, null, 0.17375, null, 0.90252, null, 0.47536, null, 33, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15516, "ERR647641", "ERX604077", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_010.fastq.gz", "fastq", 128059692.0, 5701206.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10", "0:22.46", "A:35418188;C:24802528;G:31593786;T:36245190;N:0", 22, null, null, null, 35418188, 24802528, 31593786, 36245190, 0, "ERX604077", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.72586, null, 0.1331, null, 0.92514, null, 0.4216, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15517, "ERR647637", "ERX604073", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_006.fastq.gz", "fastq", 165327404.0, 6835740.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 6", "0:24.19", "A:45252916;C:32442683;G:40306020;T:47325785;N:0", 24, null, null, null, 45252916, 32442683, 40306020, 47325785, 0, "ERX604073", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74944, null, 0.16, null, 0.91068, null, 0.47704, null, 21, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15518, "ERR647640", "ERX604076", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9", "RID0015", "Reproducibility", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_009.fastq.gz", "fastq", 134426587.0, 5846482.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9", "0:22.99", "A:36803811;C:26283055;G:33442229;T:37897492;N:0", 22, null, null, null, 36803811, 26283055, 33442229, 37897492, 0, "ERX604076", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74219, null, 0.13958, null, 0.91837, null, 0.47819, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15519, "ERR647639", "ERX604075", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8", "RID0015", "Fold Change", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0015_008.fastq.gz", "fastq", 164369360.0, 6762174.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8", "0:24.31", "A:44826982;C:33030972;G:40615427;T:45895979;N:0", 24, null, null, null, 44826982, 33030972, 40615427, 45895979, 0, "ERX604075", "ERS557914", "ERA363852", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75513, null, 0.16254, null, 0.90534, null, 0.50535, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15520, "ERR647623", "ERX604059", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_008.fastq.gz", "fastq", 198146766.0, 7373392.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8", "0:26.87", "A:50518864;C:42346985;G:50683068;T:54597849;N:0", 26, null, null, null, 50518864, 42346985, 50683068, 54597849, 0, "ERX604059", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73719, null, 0.16567, null, 0.89869, null, 0.49695, null, 76, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15521, "ERR647622", "ERX604058", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_007.fastq.gz", "fastq", 240260456.0, 9194064.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7", "0:26.13", "A:62434032;C:50861577;G:60916218;T:66048629;N:0", 26, null, null, null, 62434032, 50861577, 60916218, 66048629, 0, "ERX604058", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73042, null, 0.17017, null, 0.89509, null, 0.51784, null, 44, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15522, "ERR647620", "ERX604056", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_005.fastq.gz", "fastq", 140470735.0, 4903805.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5", "0:28.65", "A:35312706;C:29191443;G:36788541;T:39178045;N:0", 28, null, null, null, 35312706, 29191443, 36788541, 39178045, 0, "ERX604056", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.76081, null, 0.16609, null, 0.90216, null, 0.48155, null, 72, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15523, "ERR647617", "ERX604053", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_002.fastq.gz", "fastq", 113953599.0, 4875815.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2", "0:23.37", "A:29576305;C:23096908;G:29656780;T:31623606;N:0", 23, null, null, null, 29576305, 23096908, 29656780, 31623606, 0, "ERX604053", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.70891, null, 0.13528, null, 0.91208, null, 0.4622, null, 24, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15524, "ERR647624", "ERX604060", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_009.fastq.gz", "fastq", 127769435.0, 5492615.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9", "0:23.26", "A:34397217;C:25332113;G:31991788;T:36048317;N:0", 23, null, null, null, 34397217, 25332113, 31991788, 36048317, 0, "ERX604060", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.71147, null, 0.1472, null, 0.91015, null, 0.49014, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15525, "ERR647629", "ERX604065", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_014.fastq.gz", "fastq", 83983757.0, 3823842.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14", "0:21.96", "A:22501534;C:16455147;G:21619305;T:23407771;N:0", 21, null, null, null, 22501534, 16455147, 21619305, 23407771, 0, "ERX604065", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.70211, null, 0.13351, null, 0.92038, null, 0.45898, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15526, "ERR647631", "ERX604067", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_016.fastq.gz", "fastq", 117220472.0, 4272650.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16", "0:27.44", "A:29509123;C:25768315;G:30220006;T:31723028;N:0", 27, null, null, null, 29509123, 25768315, 30220006, 31723028, 0, "ERX604067", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.68585, null, 0.14679, null, 0.90778, null, 0.49492, null, 20, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15527, "ERR647618", "ERX604054", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_003.fastq.gz", "fastq", 165279016.0, 5211580.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3", "0:31.71", "A:41451579;C:36699133;G:41477197;T:45651107;N:0", 31, null, null, null, 41451579, 36699133, 41477197, 45651107, 0, "ERX604054", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.71827, null, 0.17456, null, 0.90554, null, 0.50274, null, 18, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15528, "ERR647621", "ERX604057", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_006.fastq.gz", "fastq", 181164500.0, 7686285.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6", "0:23.57", "A:48622049;C:36019225;G:45318073;T:51205153;N:0", 23, null, null, null, 48622049, 36019225, 45318073, 51205153, 0, "ERX604057", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73267, null, 0.15948, null, 0.9026, null, 0.483, null, 14, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15529, "ERR647619", "ERX604055", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_004.fastq.gz", "fastq", 131702671.0, 4688094.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4", "0:28.09", "A:32537215;C:28853793;G:34317576;T:35994087;N:0", 28, null, null, null, 32537215, 28853793, 34317576, 35994087, 0, "ERX604055", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.68635, null, 0.14911, null, 0.90532, null, 0.50027, null, 31, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15530, "ERR647628", "ERX604064", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_013.fastq.gz", "fastq", 123881257.0, 5143681.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13", "0:24.08", "A:32852368;C:25503683;G:31339781;T:34185425;N:0", 24, null, null, null, 32852368, 25503683, 31339781, 34185425, 0, "ERX604064", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.72384, null, 0.15147, null, 0.90648, null, 0.46, null, 24, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15531, "ERR647627", "ERX604063", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_012.fastq.gz", "fastq", 135155439.0, 6123293.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12", "0:22.07", "A:35870227;C:27070386;G:34401412;T:37813414;N:0", 22, null, null, null, 35870227, 27070386, 34401412, 37813414, 0, "ERX604063", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.69126, null, 0.12647, null, 0.91695, null, 0.46572, null, 25, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15532, "ERR647626", "ERX604062", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_011.fastq.gz", "fastq", 138836612.0, 5648801.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11", "0:24.58", "A:36426455;C:28359755;G:34985736;T:39064666;N:0", 24, null, null, null, 36426455, 28359755, 34985736, 39064666, 0, "ERX604062", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73565, null, 0.15718, null, 0.90382, null, 0.45772, null, 67, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15533, "ERR647625", "ERX604061", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_010.fastq.gz", "fastq", 182404716.0, 6612019.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10", "0:27.59", "A:47718609;C:38775928;G:45637186;T:50272993;N:0", 27, null, null, null, 47718609, 38775928, 45637186, 50272993, 0, "ERX604061", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75246, null, 0.19746, null, 0.88544, null, 0.48212, null, 36, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15534, "ERR647616", "ERX604052", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:086 1", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_001.fastq.gz", "fastq", 137653436.0, 5155975.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 1", "0:26.70", "A:34561717;C:29961559;G:35320222;T:37809938;N:0", 26, null, null, null, 34561717, 29961559, 35320222, 37809938, 0, "ERX604052", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.71887, null, 0.15223, null, 0.90824, null, 0.49462, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15535, "ERR647630", "ERX604066", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15", "RID0017", "EtOH conc. experiment", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0017_015.fastq.gz", "fastq", 101714594.0, 4045987.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15", "0:25.14", "A:26518632;C:20741074;G:25853629;T:28601259;N:0", 25, null, null, null, 26518632, 20741074, 25853629, 28601259, 0, "ERX604066", "ERS557914", "ERA363851", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74566, null, 0.16455, null, 0.89534, null, 0.48977, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15536, "ERR647610", "ERX604046", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", null, "ERP007147", "Ion Torrent PGM sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_009.fastq.gz", "fastq", 114880508.0, 4321457.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1", "0:26.58", "A:31499097;C:23030789;G:27803371;T:32547251;N:0", 26, null, null, null, 31499097, 23030789, 27803371, 32547251, 0, "ERX604046", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.7932, null, 0.2086, null, 0.89045, null, 0.49364, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15537, "ERR647611", "ERX604047", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_010.fastq.gz", "fastq", 124380158.0, 4885304.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2", "0:25.46", "A:33809369;C:25116497;G:30529372;T:34924920;N:0", 25, null, null, null, 33809369, 25116497, 30529372, 34924920, 0, "ERX604047", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.78302, null, 0.1944, null, 0.89398, null, 0.50469, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15538, "ERR647612", "ERX604048", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_011.fastq.gz", "fastq", 122081664.0, 4959591.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3", "0:24.62", "A:33452935;C:24151113;G:29942213;T:34535403;N:0", 24, null, null, null, 33452935, 24151113, 29942213, 34535403, 0, "ERX604048", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.77425, null, 0.18982, null, 0.8911, null, 0.46046, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15539, "ERR647615", "ERX604051", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_014.fastq.gz", "fastq", 120491210.0, 4564333.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6", "0:26.40", "A:33116448;C:24416657;G:29447901;T:33510204;N:0", 26, null, null, null, 33116448, 24416657, 29447901, 33510204, 0, "ERX604051", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.77843, null, 0.20568, null, 0.88605, null, 0.51892, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15540, "ERR647614", "ERX604050", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_013.fastq.gz", "fastq", 108193052.0, 4221217.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5", "0:25.63", "A:29795112;C:21481151;G:26281164;T:30635625;N:0", 25, null, null, null, 29795112, 21481151, 26281164, 30635625, 0, "ERX604050", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.78861, null, 0.19966, null, 0.89207, null, 0.49332, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15541, "ERR647613", "ERX604049", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4", "RID0023", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0023_012.fastq.gz", "fastq", 134807115.0, 5232713.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4", "0:25.76", "A:37141537;C:27086121;G:32486547;T:38092910;N:0", 25, null, null, null, 37141537, 27086121, 32486547, 38092910, 0, "ERX604049", "ERS557914", "ERA363850", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.78328, null, 0.20061, null, 0.88903, null, 0.51655, null, 32, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15542, "ERR647603", "ERX604039", "ERS557923", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Female 016", "SAMEA2796308", "UNIVERSITY OF AMSTERDAM", "Alias:Female 016|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557923|Sample Name:ERS557923|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_010.fastq.gz", "fastq", 186445198.0, 6054478.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8", "0:30.79", "A:51431122;C:41043403;G:44213690;T:49756983;N:0", 30, null, null, null, 51431122, 41043403, 44213690, 49756983, 0, "ERX604039", "ERS557923", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74649, null, 0.44738, null, 0.84254, null, 0.55199, null, 13, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15543, "ERR647602", "ERX604038", "ERS557922", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Female 014", "SAMEA2796307", "UNIVERSITY OF AMSTERDAM", "Alias:Female 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557922|Sample Name:ERS557922|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_009.fastq.gz", "fastq", 199860614.0, 6227225.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7", "0:32.09", "A:53999848;C:44698032;G:48251471;T:52911263;N:0", 32, null, null, null, 53999848, 44698032, 48251471, 52911263, 0, "ERX604038", "ERS557922", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.75262, null, 0.42794, null, 0.83619, null, 0.5624, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15544, "ERR647601", "ERX604037", "ERS557921", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Female 008", "SAMEA2796306", "UNIVERSITY OF AMSTERDAM", "Alias:Female 008|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557921|Sample Name:ERS557921|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_008.fastq.gz", "fastq", 190251948.0, 6082600.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6", "0:31.28", "A:50176174;C:43027879;G:47458847;T:49589048;N:0", 31, null, null, null, 50176174, 43027879, 47458847, 49589048, 0, "ERX604037", "ERS557921", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.72654, null, 0.373, null, 0.82785, null, 0.52436, null, 25, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15545, "ERR647600", "ERX604036", "ERS557920", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Female 007", "SAMEA2796305", "UNIVERSITY OF AMSTERDAM", "Alias:Female 007|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557920|Sample Name:ERS557920|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_007.fastq.gz", "fastq", 214503694.0, 6990446.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5", "0:30.69", "A:59354819;C:47472262;G:51306173;T:56370440;N:0", 30, null, null, null, 59354819, 47472262, 51306173, 56370440, 0, "ERX604036", "ERS557920", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74272, null, 0.45587, null, 0.83161, null, 0.53444, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15546, "ERR647599", "ERX604035", "ERS557919", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 014", "SAMEA2796304", "UNIVERSITY OF AMSTERDAM", "Alias:Male 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557919|Sample Name:ERS557919|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_005.fastq.gz", "fastq", 235098531.0, 7522781.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4", "0:31.25", "A:58178492;C:54009752;G:64159987;T:58750300;N:0", 31, null, null, null, 58178492, 54009752, 64159987, 58750300, 0, "ERX604035", "ERS557919", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.73752, null, 0.19698, null, 0.86665, null, 0.58697, null, 13, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15547, "ERR647598", "ERX604034", "ERS557918", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 011", "SAMEA2796303", "UNIVERSITY OF AMSTERDAM", "Alias:Male 011|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557918|Sample Name:ERS557918|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_004.fastq.gz", "fastq", 223142261.0, 6553993.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3", "0:34.05", "A:55488952;C:50941034;G:58123716;T:58588559;N:0", 34, null, null, null, 55488952, 50941034, 58123716, 58588559, 0, "ERX604034", "ERS557918", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.74686, null, 0.2139, null, 0.86996, null, 0.55375, null, 11, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15548, "ERR647597", "ERX604033", "ERS557917", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 006", "SAMEA2796302", "UNIVERSITY OF AMSTERDAM", "Alias:Male 006|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557917|Sample Name:ERS557917|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_002.fastq.gz", "fastq", 166401146.0, 5656405.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2", "0:29.42", "A:41137490;C:38824883;G:44865980;T:41572793;N:0", 29, null, null, null, 41137490, 38824883, 44865980, 41572793, 0, "ERX604033", "ERS557917", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.69452, null, 0.18245, null, 0.87044, null, 0.58162, null, 11, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15549, "ERR647596", "ERX604032", "ERS557916", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 003", "SAMEA2796301", "UNIVERSITY OF AMSTERDAM", "Alias:Male 003|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:23Z|INSDC status:public|SRA accession:ERS557916|Sample Name:ERS557916|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1", "RID0035", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0035_001.fastq.gz", "fastq", 167146177.0, 6380638.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1", "0:26.20", "A:43620211;C:36811253;G:43301042;T:43413671;N:0", 26, null, null, null, 43620211, 36811253, 43301042, 43413671, 0, "ERX604032", "ERS557916", "ERA363846", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.70048, null, 0.18034, null, 0.88075, null, 0.55658, null, 11, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15550, "ERR647595", "ERX604031", "ERS557915", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Egg", "SAMEA2796300", "UNIVERSITY OF AMSTERDAM", "Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1", "RID0024", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0024_016.fastq.gz", "fastq", 6684767188.0, 89052017.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1", "0:75.07", "A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0", 75, null, null, null, 1523328157, 1795624453, 1849675240, 1516139338, 0, "ERX604031", "ERS557915", "ERA363845", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.89536, null, 0.15322, null, 0.91421, null, 0.69019, null, 73, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [15551, "ERR647594", "ERX604030", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Male 001", "SAMEA2796299", "UNIVERSITY OF AMSTERDAM", "Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6", "RID0011", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0011_015.fastq.gz", "fastq", 273349184.0, 9019669.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6", "0:30.31", "A:74069549;C:59041449;G:64551451;T:75686735;N:0", 30, null, null, null, 74069549, 59041449, 64551451, 75686735, 0, "ERX604030", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.78759, null, 0.26081, null, 0.90989, null, 0.51416, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Adult", "Adult", "Undetermined", "Undetermined"], [15552, "ERR647589", "ERX604025", "ERS557914", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. 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