rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
15504,ERR757154,ERX701784,ERS659467,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,Normalization across length,SAMEA3251321,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251321|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female X|common name:zebrafish|dev stage:Adult|sample name:Female X|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_003.fastq.gz,fastq,275591336.0,7611054.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,0:36.21,A:72212971;C:63331647;G:68054270;T:71992448;N:0,36,,,,72212971,63331647,68054270,71992448,0,ERX701784,ERS659467,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76262,,0.4273,,0.8101,,0.56676,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15505,ERR757153,ERX701783,ERS659466,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,Normalization across length,SAMEA3251320,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251320|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female 002|common name:zebrafish|dev stage:Adult|sample name:Female 002|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_006.fastq.gz,fastq,193706106.0,6343893.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,0:30.53,A:52756888;C:42895374;G:46979869;T:51073975;N:0,30,,,,52756888,42895374,46979869,51073975,0,ERX701783,ERS659466,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74991,,0.41319,,0.83002,,0.55823,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15506,ERR647638,ERX604074,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,49408107,35660562,44520624,51896050,0,ERX604074,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75831,,0.16017,,0.90723,,0.48684,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15507,ERR647632,ERX604068,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_001.fastq.gz,fastq,158714692.0,5407747.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,0:29.35,A:42098161;C:32991434;G:38596553;T:45028544;N:0,29,,,,42098161,32991434,38596553,45028544,0,ERX604068,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75901,,0.20293,,0.89505,,0.48215,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15508,ERR647636,ERX604072,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_005.fastq.gz,fastq,124167412.0,4838491.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,0:25.66,A:33439510;C:24728035;G:30897675;T:35102192;N:0,25,,,,33439510,24728035,30897675,35102192,0,ERX604072,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76027,,0.17783,,0.89692,,0.48421,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15509,ERR647635,ERX604071,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_004.fastq.gz,fastq,124786630.0,4701452.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,0:26.54,A:33803418;C:24800330;G:30482560;T:35700322;N:0,26,,,,33803418,24800330,30482560,35700322,0,ERX604071,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74872,,0.18448,,0.89789,,0.50377,,12,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15510,ERR647634,ERX604070,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_003.fastq.gz,fastq,110526752.0,4078127.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,0:27.10,A:29453167;C:22981184;G:27444083;T:30648318;N:0,27,,,,29453167,22981184,27444083,30648318,0,ERX604070,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73961,,0.1804,,0.89686,,0.50069,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15511,ERR647633,ERX604069,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_002.fastq.gz,fastq,114721515.0,4468497.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,0:25.67,A:31387085;C:22123581;G:28270438;T:32940411;N:0,25,,,,31387085,22123581,28270438,32940411,0,ERX604069,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75767,,0.17199,,0.90118,,0.49949,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15512,ERR647645,ERX604081,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,35700746,25577569,31187339,35277288,0,ERX604081,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72451,,0.1507,,0.91078,,0.47283,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,48008107,34657005,43047489,49607271,0,ERX604080,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75539,,0.16288,,0.90388,,0.47538,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,48143286,36300870,44060167,48939429,0,ERX604079,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74839,,0.15018,,0.90782,,0.49076,,27,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,44540588,32608476,40066295,46174014,0,ERX604078,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75948,,0.17375,,0.90252,,0.47536,,33,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,35418188,24802528,31593786,36245190,0,ERX604077,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72586,,0.1331,,0.92514,,0.4216,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,45252916,32442683,40306020,47325785,0,ERX604073,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74944,,0.16,,0.91068,,0.47704,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,36803811,26283055,33442229,37897492,0,ERX604076,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74219,,0.13958,,0.91837,,0.47819,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,44826982,33030972,40615427,45895979,0,ERX604075,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75513,,0.16254,,0.90534,,0.50535,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,50518864,42346985,50683068,54597849,0,ERX604059,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73719,,0.16567,,0.89869,,0.49695,,76,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,62434032,50861577,60916218,66048629,0,ERX604058,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73042,,0.17017,,0.89509,,0.51784,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,35312706,29191443,36788541,39178045,0,ERX604056,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76081,,0.16609,,0.90216,,0.48155,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,29576305,23096908,29656780,31623606,0,ERX604053,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70891,,0.13528,,0.91208,,0.4622,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,34397217,25332113,31991788,36048317,0,ERX604060,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71147,,0.1472,,0.91015,,0.49014,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,22501534,16455147,21619305,23407771,0,ERX604065,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70211,,0.13351,,0.92038,,0.45898,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,29509123,25768315,30220006,31723028,0,ERX604067,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68585,,0.14679,,0.90778,,0.49492,,20,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,41451579,36699133,41477197,45651107,0,ERX604054,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71827,,0.17456,,0.90554,,0.50274,,18,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,48622049,36019225,45318073,51205153,0,ERX604057,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73267,,0.15948,,0.9026,,0.483,,14,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,32537215,28853793,34317576,35994087,0,ERX604055,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68635,,0.14911,,0.90532,,0.50027,,31,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,32852368,25503683,31339781,34185425,0,ERX604064,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72384,,0.15147,,0.90648,,0.46,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,35870227,27070386,34401412,37813414,0,ERX604063,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69126,,0.12647,,0.91695,,0.46572,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,36426455,28359755,34985736,39064666,0,ERX604062,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73565,,0.15718,,0.90382,,0.45772,,67,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,47718609,38775928,45637186,50272993,0,ERX604061,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75246,,0.19746,,0.88544,,0.48212,,36,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:086 1,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,34561717,29961559,35320222,37809938,0,ERX604052,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71887,,0.15223,,0.90824,,0.49462,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,26518632,20741074,25853629,28601259,0,ERX604066,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74566,,0.16455,,0.89534,,0.48977,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent PGM sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,,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,,,,31499097,23030789,27803371,32547251,0,ERX604046,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.7932,,0.2086,,0.89045,,0.49364,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,33809369,25116497,30529372,34924920,0,ERX604047,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78302,,0.1944,,0.89398,,0.50469,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,33452935,24151113,29942213,34535403,0,ERX604048,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77425,,0.18982,,0.8911,,0.46046,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,33116448,24416657,29447901,33510204,0,ERX604051,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77843,,0.20568,,0.88605,,0.51892,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,29795112,21481151,26281164,30635625,0,ERX604050,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78861,,0.19966,,0.89207,,0.49332,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,37141537,27086121,32486547,38092910,0,ERX604049,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78328,,0.20061,,0.88903,,0.51655,,32,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,51431122,41043403,44213690,49756983,0,ERX604039,ERS557923,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74649,,0.44738,,0.84254,,0.55199,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,53999848,44698032,48251471,52911263,0,ERX604038,ERS557922,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75262,,0.42794,,0.83619,,0.5624,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,50176174,43027879,47458847,49589048,0,ERX604037,ERS557921,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72654,,0.373,,0.82785,,0.52436,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,59354819,47472262,51306173,56370440,0,ERX604036,ERS557920,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74272,,0.45587,,0.83161,,0.53444,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,58178492,54009752,64159987,58750300,0,ERX604035,ERS557919,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73752,,0.19698,,0.86665,,0.58697,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,55488952,50941034,58123716,58588559,0,ERX604034,ERS557918,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74686,,0.2139,,0.86996,,0.55375,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,41137490,38824883,44865980,41572793,0,ERX604033,ERS557917,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69452,,0.18245,,0.87044,,0.58162,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,43620211,36811253,43301042,43413671,0,ERX604032,ERS557916,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70048,,0.18034,,0.88075,,0.55658,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,74069549,59041449,64551451,75686735,0,ERX604030,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78759,,0.26081,,0.90989,,0.51416,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,16624629,13894132,10557585,13575346,0,ERX604025,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.11072,,0.02655,,0.97749,,0.53916,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,12984359,11329853,10330928,12406050,0,ERX604026,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.36871,,0.10094,,0.9483,,0.51008,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,108705027,84131955,92090437,109884640,0,ERX604028,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.65205,,0.21183,,0.91977,,0.52643,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,38374880,31424768,33687670,39751488,0,ERX604029,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78469,,0.26587,,0.92178,,0.51694,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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 10–300 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.,,,,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,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,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,,,,16076639,14164415,11139997,14160123,0,ERX604027,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.16692,,0.04528,,0.96384,,0.52823,,17,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,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,,,egg pools from three different mothers,,Egg pool Dr,,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,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,94 4,94 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0094BC04smallZF.fastq,fastq,1392075126.0,18333358.0,eggRID0094BC04smallZF.fastq,0:75.93,A:323480979;C:386272283;G:377777594;T:304544270;N:0,75,,,,323480979,386272283,377777594,304544270,0,SRX2245300,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.68028,,0.1685,,0.89982,,0.84521,,83,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
41424,SRR4423112,SRX2245296,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,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,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,88 4,88 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0088BC04smallZF.fastq,fastq,1063934659.0,14422089.0,eggRID0088BC04smallZF.fastq,0:73.77,A:248885216;C:293368431;G:288043879;T:233637133;N:0,73,,,,248885216,293368431,288043879,233637133,0,SRX2245296,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.66115,,0.18031,,0.89546,,0.78468,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
41426,SRR4423110,SRX2245294,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,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,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,93 4,93 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0093BC04smallZF.fastq,fastq,1382951404.0,18190154.0,eggRID0093BC04smallZF.fastq,0:76.03,A:322536095;C:383176934;G:374216039;T:303022336;N:0,76,,,,322536095,383176934,374216039,303022336,0,SRX2245294,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.66399,,0.17461,,0.90134,,0.82432,,156,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined