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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. 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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"], [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. 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 1", "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_010.fastq.gz", "fastq", 54651692.0, 2000589.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1", "0:27.32", "A:16624629;C:13894132;G:10557585;T:13575346;N:0", 27, null, null, null, 16624629, 13894132, 10557585, 13575346, 0, "ERX604025", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.11072, null, 0.02655, null, 0.97749, null, 0.53916, null, 26, 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"], [15553, "ERR647590", "ERX604026", "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 2", "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_011.fastq.gz", "fastq", 47051190.0, 1414933.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2", "0:33.25", "A:12984359;C:11329853;G:10330928;T:12406050;N:0", 33, null, null, null, 12984359, 11329853, 10330928, 12406050, 0, "ERX604026", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.36871, null, 0.10094, null, 0.9483, null, 0.51008, null, 40, 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"], [15554, "ERR647592", "ERX604028", "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 4", "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_013.fastq.gz", "fastq", 394812059.0, 13329274.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4", "0:29.62", "A:108705027;C:84131955;G:92090437;T:109884640;N:0", 29, null, null, null, 108705027, 84131955, 92090437, 109884640, 0, "ERX604028", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.65205, null, 0.21183, null, 0.91977, null, 0.52643, 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"], [15555, "ERR647593", "ERX604029", "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 5", "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_014.fastq.gz", "fastq", 143238806.0, 4225461.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5", "0:33.90", "A:38374880;C:31424768;G:33687670;T:39751488;N:0", 33, null, null, null, 38374880, 31424768, 33687670, 39751488, 0, "ERX604029", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.78469, null, 0.26587, null, 0.92178, null, 0.51694, null, 80, 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"], [15556, "ERR647591", "ERX604027", "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 3", "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_012.fastq.gz", "fastq", 55541174.0, 1649692.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3", "0:33.67", "A:16076639;C:14164415;G:11139997;T:14160123;N:0", 33, null, null, null, 16076639, 14164415, 11139997, 14160123, 0, "ERX604027", "ERS557914", "ERA363842", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.16692, null, 0.04528, null, 0.96384, null, 0.52823, null, 17, 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"], [41420, "SRR4423116", "SRX2245300", "SRS1745858", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, "egg pools from three different mothers", null, "Egg pool Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: Egg pool", "94 4", "94 4", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "oblong", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", null, "tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "GSM4591066", "GSM4591066: small RNA oblong 2; Danio rerio; OTHER", "GSM4591066", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "oblong", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", null, "tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "GSM4591065", "GSM4591065: small RNA oblong 1; Danio rerio; OTHER", "GSM4591065", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", "GEO Accession:GSM4591065", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent S5", null, "SRP265951", null, null, "small_RNA_oblong_stage_1.fastq", "fastq", 90701340.0, 2141489.0, "GSM4591065 r1", "0:42.35", "A:25203959;C:24291162;G:23143516;T:18062703;N:0", 42, null, null, null, 25203959, 24291162, 23143516, 18062703, 0, "SRX8469998", "SRS6770649", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.48132, null, 0.15952, null, 0.8756, null, 0.56134, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [59499, "SRR11924325", "SRX8469997", "SRS6770648", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "small RNA 32 cell", "GSM4591064", null, "source name:32 cell stage|tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "small RNA 32 cell", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", null, "tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "GSM4591064", "GSM4591064: small RNA 32 cell; Danio rerio; OTHER", "GSM4591064", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", "GEO Accession:GSM4591064", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent S5", null, "SRP265951", null, null, "small_RNA_32_cell_stage.fastq", "fastq", 275040056.0, 6091077.0, "GSM4591064 r1", "0:45.15", "A:69136092;C:69806677;G:72527986;T:63569301;N:0", 45, null, null, null, 69136092, 69806677, 72527986, 63569301, 0, "SRX8469997", "SRS6770648", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.67676, null, 0.30881, null, 0.86636, null, 0.63482, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [59500, "SRR11924324", "SRX8469996", "SRS6770647", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "small RNA 15E", "GSM4591063", null, "source name:zfs:0000015|tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "small RNA 15E", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "zfs:0000015", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", null, "tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "GSM4591063", "GSM4591063: small RNA 15E; Danio rerio; OTHER", "GSM4591063", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", "GEO Accession:GSM4591063", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent S5", null, "SRP265951", null, null, "small_RNA_15E_stage.fastq", "fastq", 264453879.0, 5777826.0, "GSM4591063 r1", "0:45.77", "A:63859672;C:67381369;G:71681258;T:61531580;N:0", 45, null, null, null, 63859672, 67381369, 71681258, 61531580, 0, "SRX8469996", "SRS6770647", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.60375, null, 0.23463, null, 0.87606, null, 0.58681, null, 40, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [59503, "SRR11924320", "SRX8469993", "SRS6770644", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "PM 3", "GSM4591060", null, "source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "PM 3", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "protruding mouth stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591060", "GSM4591060: PM 3; Danio rerio; OTHER", "GSM4591060", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591060", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa PM_3.bam", "bam bam", 215125332.0, 6403488.0, "GSM4591060 r1", "0:33.60", "A:50202267;C:65116674;G:52637331;T:47169060;N:0", 33, null, null, null, 50202267, 65116674, 52637331, 47169060, 0, "SRX8469993", "SRS6770644", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.73594, null, 0.21617, null, 0.86251, null, 0.68892, null, 42, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Larval", "Larval", "Undetermined", "Undetermined"], [59504, "SRR11924318", "SRX8469992", "SRS6770643", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "PM 2", "GSM4591059", null, "source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "PM 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "protruding mouth stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591059", "GSM4591059: PM 2; Danio rerio; OTHER", "GSM4591059", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591059", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa PM_2.bam", "bam bam", 426315355.0, 12915702.0, "GSM4591059 r1", "0:33.01", "A:92276988;C:141702085;G:104175159;T:88161123;N:0", 33, null, null, null, 92276988, 141702085, 104175159, 88161123, 0, "SRX8469992", "SRS6770643", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.76385, null, 0.1921, null, 0.87207, null, 0.71495, null, 40, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Larval", "Larval", "Undetermined", "Undetermined"], [59505, "SRR11924317", "SRX8469990", "SRS6770641", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "PM 1", "GSM4591058", null, "source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "PM 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "protruding mouth stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591058", "GSM4591058: PM 1; Danio rerio; OTHER", "GSM4591058", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591058", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa PM_1.bam", "bam bam", 130388595.0, 5124384.0, "GSM4591058 r1", "0:25.44", "A:27290253;C:42592303;G:31075292;T:29430747;N:0", 25, null, null, null, 27290253, 42592303, 31075292, 29430747, 0, "SRX8469990", "SRS6770641", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.78884, null, 0.23004, null, 0.85113, null, 0.67571, null, 38, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Larval", "Larval", "Undetermined", "Undetermined"], [59506, "SRR11924315", "SRX8469989", "SRS6770640", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "12 somite 3", "GSM4591057", null, "source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "12 somite 3", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591057", "GSM4591057: 12 somite 3; Danio rerio; OTHER", "GSM4591057", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591057", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "12_somite_3.bam GSE151797_Reference_sequence.fa", "bam bam", 105146264.0, 3189309.0, "GSM4591057 r1", "0:32.97", "A:24684898;C:33906144;G:26247070;T:20308152;N:0", 32, null, null, null, 24684898, 33906144, 26247070, 20308152, 0, "SRX8469989", "SRS6770640", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.83304, null, 0.22816, null, 0.88325, null, 0.69597, null, 43, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Segmentation", "Embryo", "Undetermined", "Embryo Imprecise"], [59507, "SRR11924314", "SRX8469988", "SRS6770639", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "12 somite 2", "GSM4591056", null, "source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "12 somite 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591056", "GSM4591056: 12 somite 2; Danio rerio; OTHER", "GSM4591056", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591055", "GSM4591055: 12 somite 1; Danio rerio; OTHER", "GSM4591055", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591054", "GSM4591054: 32 cell 3; Danio rerio; OTHER", "GSM4591054", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591053", "GSM4591053: 32 cell 2; Danio rerio; OTHER", "GSM4591053", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. 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Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591052", "GSM4591052: 32 cell 1; Danio rerio; OTHER", "GSM4591052", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. 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