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
36560,SRR1048073,SRX363298,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish Brain miRNA,Brain miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,ZB_trimmed.fastq,fastq,323899236.0,14781569.0,Brain miRNA run,0:21.91 1:0,A:77705253;C:63882329;G:85902986;T:96383552;N:25116,21,0,,,77705253,63882329,85902986,96383552,25116,SRX363298,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.88754,,0.06569,,0.96747,,0.53358,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
36561,SRR1048072,SRX363297,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark miRNA,Pineal gland dark miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,D_trimmed.fastq,fastq,231371620.0,10385264.0,Pineal gland dark miRNA run,0:22.28 1:0,A:61228408;C:44264639;G:58700027;T:67159878;N:18668,22,0,,,61228408,44264639,58700027,67159878,18668,SRX363297,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.84648,,0.04467,,0.95645,,0.79978,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
36562,SRR1048071,SRX363296,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light miRNA,Pineal gland light miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,L_trimmed.fastq,fastq,132417471.0,5933638.0,Pineal gland light miRNA run,0:22.32 1:0,A:36017069;C:26569684;G:32546616;T:37273526;N:10576,22,0,,,36017069,26569684,32546616,37273526,10576,SRX363296,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.86427,,0.03426,,0.95631,,0.86509,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
37921,SRR1554495,SRX685396,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_3.fq.gz,fastq,1225610154.0,12134754.0,Ovary2 Run3,0:101,A:347141358;C:303255805;G:280185540;T:294456010;N:571441,101,,,,347141358,303255805,280185540,294456010,571441,SRX685396,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37922,SRR1554492,SRX685395,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_3.fq.gz,fastq,1192024422.0,11802222.0,Testis2 Run3,0:101,A:373380865;C:276125943;G:251033102;T:290931637;N:552875,101,,,,373380865,276125943,251033102,290931637,552875,SRX685395,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,1e-05,,0.99997,,0.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37923,SRR1554489,SRX685394,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_3.fq.gz,fastq,1302765670.0,12898670.0,Heart2 Run3,0:101,A:397689061;C:312745449;G:268626802;T:323141419;N:562939,101,,,,397689061,312745449,268626802,323141419,562939,SRX685394,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37924,SRR1554486,SRX685392,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_3.fq.gz,fastq,1211892536.0,11998936.0,Brain2 Run3,0:101,A:374228993;C:286134640;G:253944548;T:297038575;N:545780,101,,,,374228993,286134640,253944548,297038575,545780,SRX685392,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37925,SRR1554483,SRX685391,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_3.fq.gz,fastq,347516154.0,3440754.0,Ovary1 Run3,0:101,A:107805981;C:80183725;G:73617313;T:85763181;N:145954,101,,,,107805981,80183725,73617313,85763181,145954,SRX685391,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,4e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37926,SRR1554480,SRX685390,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_3.fq.gz,fastq,1184228636.0,11725036.0,Testis1 Run3,0:101,A:340636900;C:278505979;G:259975802;T:304564724;N:545231,101,,,,340636900,278505979,259975802,304564724,545231,SRX685390,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,1e-05,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37927,SRR1554477,SRX685389,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_3.fq.gz,fastq,1561371524.0,15459124.0,Heart1 Run3,0:101,A:454757966;C:391143691;G:334715236;T:380114024;N:640607,101,,,,454757966,391143691,334715236,380114024,640607,SRX685389,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37928,SRR1554474,SRX685388,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_3.fq.gz,fastq,1192445794.0,11806394.0,Brain1 Run3,0:101,A:369786121;C:268557682;G:265557417;T:288006805;N:537769,101,,,,369786121,268557682,265557417,288006805,537769,SRX685388,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37929,SRR1554493,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_1.fq.gz,fastq,476104278.0,9335378.0,Ovary2 Run1,0:51,A:111060704;C:120863975;G:129849761;T:114224677;N:105161,51,,,,111060704,120863975,129849761,114224677,105161,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00027,,8e-05,,0.99945,,0.8125,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37930,SRR1554494,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF4_Ovary_2.fq.gz,fastq,561956352.0,11018752.0,Ovary2 Run2,0:51,A:129925815;C:148479658;G:148478706;T:132824290;N:2247883,51,,,,129925815,148479658,148478706,132824290,2247883,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,0.0001,,0.99967,,0.6875,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37931,SRR1554490,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_1.fq.gz,fastq,586152231.0,11493181.0,Testis2 Run1,0:51,A:145360493;C:148943988;G:151402108;T:140286245;N:159397,51,,,,145360493,148943988,151402108,140286245,159397,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37932,SRR1554491,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Testis_2.fq.gz,fastq,697016337.0,13666987.0,Testis2 Run2,0:51,A:172082858;C:184634425;G:173370430;T:163527914;N:3400710,51,,,,172082858,184634425,173370430,163527914,3400710,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37933,SRR1554487,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_1.fq.gz,fastq,767836212.0,15055612.0,Heart2 Run1,0:51,A:192620363;C:202013249;G:191038597;T:181862075;N:301928,51,,,,192620363,202013249,191038597,181862075,301928,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,3e-05,,0.99995,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37934,SRR1554488,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Heart_2.fq.gz,fastq,979886205.0,19213455.0,Heart2 Run2,0:51,A:246169086;C:264387065;G:236377487;T:227289693;N:5662874,51,,,,246169086,264387065,236377487,227289693,5662874,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37935,SRR1554484,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_1.fq.gz,fastq,654412671.0,12831621.0,Brain2 Run1,0:51,A:160544180;C:166355290;G:168608762;T:158684308;N:220131,51,,,,160544180,166355290,168608762,158684308,220131,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,0.0,,0.99993,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37936,SRR1554485,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF2_Brain_2.fq.gz,fastq,856322793.0,16790643.0,Brain2 Run2,0:51,A:210706815;C:226772546;G:212404752;T:201722093;N:4716587,51,,,,210706815,226772546,212404752,201722093,4716587,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37937,SRR1554481,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_1.fq.gz,fastq,116086965.0,2276215.0,Ovary1 Run1,0:51,A:29237121;C:30235277;G:29264328;T:27320814;N:29425,51,,,,29237121,30235277,29264328,27320814,29425,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,9e-05,,0.99967,,0.65,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37938,SRR1554482,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF3_Ovary_2.fq.gz,fastq,138905844.0,2723644.0,Ovary1 Run2,0:51,A:34695180;C:38015933;G:33434207;T:32057083;N:703441,51,,,,34695180,38015933,33434207,32057083,703441,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00016,,5e-05,,0.99977,,0.42857,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37939,SRR1554478,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_1.fq.gz,fastq,655515750.0,12853250.0,Testis1 Run1,0:51,A:152422885;C:163771947;G:179144090;T:159997538;N:179290,51,,,,152422885,163771947,179144090,159997538,179290,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0011,,0.00053,,0.99829,,0.67777,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37940,SRR1554479,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Testis_2.fq.gz,fastq,777594399.0,15246949.0,Testis1 Run2,0:51,A:180116528;C:202508153;G:204833105;T:186435696;N:3700917,51,,,,180116528,202508153,204833105,186435696,3700917,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00073,,0.00032,,0.99898,,0.62745,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37941,SRR1554475,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_1.fq.gz,fastq,810162642.0,15885542.0,Heart1 Run1,0:51,A:199665102;C:213941735;G:204361738;T:191870055;N:324012,51,,,,199665102,213941735,204361738,191870055,324012,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,6e-05,,1e-05,,0.99989,,0.8,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37942,SRR1554476,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Heart_2.fq.gz,fastq,1013563698.0,19873798.0,Heart1 Run2,0:51,A:249913434;C:275453651;G:247166233;T:235034199;N:5996181,51,,,,249913434,275453651,247166233,235034199,5996181,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,4e-05,,2e-05,,0.99997,,0.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37943,SRR1554472,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_1.fq.gz,fastq,679860294.0,13330594.0,Brain1 Run1,0:51,A:167202435;C:176450132;G:174468721;T:161497185;N:241821,51,,,,167202435,176450132,174468721,161497185,241821,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37944,SRR1554473,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP039502,,,ZF1_Brain_2.fq.gz,fastq,838372782.0,16438682.0,Brain1 Run2,0:51,A:206906228;C:221202670;G:210716690;T:195319694;N:4227500,51,,,,206906228,221202670,210716690,195319694,4227500,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
38046,SRR1427469,SRX612649,SRS643610,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,28d,GSM1417152,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,28d,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417152,GSM1417152: 28d; Danio rerio; miRNA Seq,GSM1417152,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417152,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,28d.fq,bam,694299184.0,32089203.0,GSM1417152 r1,0:21.64 1:0,A:174747494;C:132129648;G:193085254;T:194336788;N:0,21,0,,,174747494,132129648,193085254,194336788,0,SRX612649,SRS643610,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.93434,,0.05272,,0.98831,,0.56642,,23,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
38047,SRR1427468,SRX612648,SRS643609,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,72h,GSM1417151,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,72h,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417151,GSM1417151: 72h; Danio rerio; miRNA Seq,GSM1417151,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417151,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,72h.fq,fastq,689263089.0,31419317.0,GSM1417151 r1,0:21.94 1:0,A:161567060;C:125003691;G:193763870;T:208928468;N:0,21,0,,,161567060,125003691,193763870,208928468,0,SRX612648,SRS643609,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.93237,,0.03751,,0.98774,,0.51765,,20,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
38048,SRR1427467,SRX612647,SRS643608,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,0h,GSM1417150,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,0h,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417150,GSM1417150: 0h; Danio rerio; miRNA Seq,GSM1417150,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417150,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,0h.bam,fastq,3005859202.0,134278309.0,GSM1417150 r1,0:22.39,A:762111385;C:628084257;G:836553469;T:779110091;N:0,22,,,,762111385,628084257,836553469,779110091,0,SRX612647,SRS643608,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.94362,,0.03903,,0.99093,,0.5848,,22,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
39609,SRR1873571,SRX915251,SRS870223,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,fins,GSM1630515,,source name:adult fins 1 year old|strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year,fins,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult fins 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year,GSM1630515,GSM1630515: fins; Danio rerio; miRNA Seq,GSM1630515,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630515,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,113161.0,2108.0,GSM1630515 r1,0:4 1:49.68,A:30303;C:30710;G:27210;T:24785;N:153,4,49,,,30303,30710,27210,24785,153,SRX915251,SRS870223,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,50,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Fin,Surface Structure
39610,SRR1873570,SRX915250,SRS870224,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,skin,GSM1630514,,source name:adult skin 1 year old|strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year,skin,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult skin 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year,GSM1630514,GSM1630514: skin; Danio rerio; miRNA Seq,GSM1630514,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630514,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,79232.0,1527.0,GSM1630514 r1,0:4 1:47.89,A:20622;C:23508;G:19017;T:15967;N:118,4,47,,,20622,23508,19017,15967,118,SRX915250,SRS870224,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,53,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Skin,Surface Structure
39611,SRR1873569,SRX915249,SRS870225,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,heart,GSM1630513,,source name:adult heart 1 year old|strain/background:AB|genotype/variation:wild type|tissue:heart|developmental stage:adult|age:1 year,heart,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult heart 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:heart|developmental stage:adult|age:1 year,GSM1630513,GSM1630513: heart; Danio rerio; miRNA Seq,GSM1630513,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630513,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,39500.0,711.0,GSM1630513 r1,0:4 1:51.56,A:11300;C:9125;G:9195;T:9835;N:45,4,51,,,11300,9125,9195,9835,45,SRX915249,SRS870225,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,53,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Heart,Cardiovascular System
39612,SRR1873568,SRX915248,SRS870226,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,gills,GSM1630512,,source name:adult gills 1 year old|strain/background:AB|genotype/variation:wild type|tissue:gills|developmental stage:adult|age:1 year,gills,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult gills 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:gills|developmental stage:adult|age:1 year,GSM1630512,GSM1630512: gills; Danio rerio; miRNA Seq,GSM1630512,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630512,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,189248.0,3563.0,GSM1630512 r1,0:4 1:49.11,A:48212;C:55198;G:44765;T:40711;N:362,4,49,,,48212,55198,44765,40711,362,SRX915248,SRS870226,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,44,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Gill,Respiratory System
39613,SRR1873567,SRX915247,SRS870227,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,eyes,GSM1630511,,source name:adult eyes 1 year old|strain/background:AB|genotype/variation:wild type|tissue:eyes|developmental stage:adult|age:1 year,eyes,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult eyes 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:eyes|developmental stage:adult|age:1 year,GSM1630511,GSM1630511: eyes; Danio rerio; miRNA Seq,GSM1630511,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630511,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,173069.0,3135.0,GSM1630511 r1,0:4 1:51.21,A:50732;C:44705;G:40960;T:36324;N:348,4,51,,,50732,44705,40960,36324,348,SRX915247,SRS870227,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,52,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Eye,Sensory System
39614,SRR1873566,SRX915246,SRS870228,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,brain,GSM1630510,,source name:adult brain 1 year old|strain/background:AB|genotype/variation:wild type|tissue:brain|developmental stage:adult|age:1 year,brain,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult brain 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:brain|developmental stage:adult|age:1 year,GSM1630510,GSM1630510: brain; Danio rerio; miRNA Seq,GSM1630510,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630510,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,688279.0,12620.0,GSM1630510 r1,0:4 1:50.54,A:205782;C:180028;G:171745;T:129693;N:1031,4,50,,,205782,180028,171745,129693,1031,SRX915246,SRS870228,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,48,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Brain,Nervous System
39615,SRR1873565,SRX915245,SRS870229,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,adult,GSM1630509,,source name:entire adult|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,adult,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,entire adult,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,GSM1630509,GSM1630509: adult; Danio rerio; miRNA Seq,GSM1630509,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630509,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,361024.0,6498.0,GSM1630509 r1,0:4 1:51.56,A:104704;C:84406;G:83224;T:87843;N:847,4,51,,,104704,84406,83224,87843,847,SRX915245,SRS870229,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Trunk,Surface Structure
41418,SRR4423118,SRX2245302,SRS1745860,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult FT Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult female tail,172 5,172 5,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,,,femaletailRID0172BC05smallZF.fastq,fastq,491055734.0,7690105.0,femaletailRID0172BC05smallZF.fastq,0:63.86,A:114732043;C:132287469;G:130972143;T:113064079;N:0,63,,,,114732043,132287469,130972143,113064079,0,SRX2245302,SRS1745860,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.82246,,0.13521,,0.91303,,0.63226,,43,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Tail,Multi-system
41421,SRR4423115,SRX2245299,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,94 3,94 3,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,,,maleRID0094BC03smallZF.fastq,fastq,697814234.0,14408051.0,maleRID0094BC03smallZF.fastq,0:48.43,A:165337411;C:177790468;G:184204311;T:170482044;N:0,48,,,,165337411,177790468,184204311,170482044,0,SRX2245299,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70426,,0.16215,,0.91027,,0.5459,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41425,SRR4423111,SRX2245295,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,88 3,88 3,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,,,maleRID0088BC03smallZF.fastq,fastq,523776538.0,11118832.0,maleRID0088BC03smallZF.fastq,0:47.11,A:123827431;C:133478804;G:138882662;T:127587641;N:0,47,,,,123827431,133478804,138882662,127587641,0,SRX2245295,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.69556,,0.16368,,0.9093,,0.54838,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41427,SRR4423109,SRX2245293,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,93 3,93 3,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,,,maleRID0093BC03smallZF.fastq,fastq,692750598.0,14286031.0,maleRID0093BC03smallZF.fastq,0:48.49,A:164412063;C:176380331;G:182539801;T:169418403;N:0,48,,,,164412063,176380331,182539801,169418403,0,SRX2245293,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70738,,0.16645,,0.90948,,0.55306,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
43050,SRR5883565,SRX3049654,SRS2396336,SRP114397,PRJNA396509,The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.,GSE102059,Transcriptome Analysis,Exposure to bisphenol A BPA  an endocrine disruptor ED  has raised concerns for both human and ecosystem health. Epigenetic factors  including microRNAs  are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model  we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA  RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver  6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes  signatures associated with non alcoholic fatty liver disease NAFLD  oxidative phosphorylation  mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29027980,,Liver BPA 4 6,GSM2722577,,tissue:Liver|exposure:100 nM BPA,Liver BPA 4 6,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output.  CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5  contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups  two containing water with 100 nM BPA  and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared  from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system.  Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,exposure:100 nM BPA,GSM2722577,GSM2722577: Liver BPA 4 6; Danio rerio; miRNA Seq,GSM2722577,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2722577,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114397,,,12_GGTAGC_LALL_R1_001.fastq.gz,fastq,461508486.0,9049186.0,GSM2722577 r1,0:51,A:92718489;C:120118265;G:143926288;T:103539215;N:1206229,51,,,,92718489,120118265,143926288,103539215,1206229,SRX3049654,SRS2396336,SRA594837,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.02792,,0.00247,,0.99602,,0.60254,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-07-31,Undetermined,Adult,Liver,Liver and Biliary System
43051,SRR5883564,SRX3049653,SRS2396335,SRP114397,PRJNA396509,The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.,GSE102059,Transcriptome Analysis,Exposure to bisphenol A BPA  an endocrine disruptor ED  has raised concerns for both human and ecosystem health. Epigenetic factors  including microRNAs  are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model  we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA  RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver  6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes  signatures associated with non alcoholic fatty liver disease NAFLD  oxidative phosphorylation  mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29027980,,Liver BPA 1 3,GSM2722576,,tissue:Liver|exposure:100 nM BPA,Liver BPA 1 3,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output.  CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5  contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups  two containing water with 100 nM BPA  and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared  from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system.  Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,exposure:100 nM BPA,GSM2722576,GSM2722576: Liver BPA 1 3; Danio rerio; miRNA Seq,GSM2722576,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2722576,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114397,,,11_GAGTGG_LALL_R1_001.fastq.gz,fastq,587697684.0,11523484.0,GSM2722576 r1,0:51,A:131489823;C:140167421;G:171253226;T:143217998;N:1569216,51,,,,131489823,140167421,171253226,143217998,1569216,SRX3049653,SRS2396335,SRA594837,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.03603,,0.00774,,0.98492,,0.65361,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-07-31,Undetermined,Adult,Liver,Liver and Biliary System
43052,SRR5883563,SRX3049652,SRS2396334,SRP114397,PRJNA396509,The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.,GSE102059,Transcriptome Analysis,Exposure to bisphenol A BPA  an endocrine disruptor ED  has raised concerns for both human and ecosystem health. Epigenetic factors  including microRNAs  are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model  we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA  RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver  6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes  signatures associated with non alcoholic fatty liver disease NAFLD  oxidative phosphorylation  mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29027980,,Liver CNTRL 4 5,GSM2722575,,tissue:Liver|exposure:Control,Liver CNTRL 4 5,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output.  CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5  contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups  two containing water with 100 nM BPA  and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared  from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system.  Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,exposure:Control,GSM2722575,GSM2722575: Liver CNTRL 4 5; Danio rerio; miRNA Seq,GSM2722575,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2722575,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114397,,,10_CGTACG_LALL_R1_001.fastq.gz,fastq,407289621.0,7986071.0,GSM2722575 r1,0:51,A:84982391;C:104532595;G:122785928;T:93918201;N:1070506,51,,,,84982391,104532595,122785928,93918201,1070506,SRX3049652,SRS2396334,SRA594837,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.13902,,0.01445,,0.99086,,0.57915,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-07-31,Undetermined,Adult,Liver,Liver and Biliary System
43053,SRR5883562,SRX3049651,SRS2396333,SRP114397,PRJNA396509,The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.,GSE102059,Transcriptome Analysis,Exposure to bisphenol A BPA  an endocrine disruptor ED  has raised concerns for both human and ecosystem health. Epigenetic factors  including microRNAs  are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model  we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA  RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver  6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes  signatures associated with non alcoholic fatty liver disease NAFLD  oxidative phosphorylation  mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29027980,,Liver CNTRL 1 3,GSM2722574,,tissue:Liver|exposure:Control,Liver CNTRL 1 3,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output.  CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5  contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups  two containing water with 100 nM BPA  and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared  from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system.  Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,exposure:Control,GSM2722574,GSM2722574: Liver CNTRL 1 3; Danio rerio; miRNA Seq,GSM2722574,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2722574,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114397,,,9_GTTTCG_LALL_R1_001.fastq.gz,fastq,379997073.0,7450923.0,GSM2722574 r1,0:51,A:79538003;C:96525448;G:113901755;T:89020494;N:1011373,51,,,,79538003,96525448,113901755,89020494,1011373,SRX3049651,SRS2396333,SRA594837,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.00447,,0.0005,,0.99626,,0.57217,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-07-31,Undetermined,Adult,Liver,Liver and Biliary System
44999,SRR6411468,SRX3504483,SRS2782037,SRP127389,PRJNA427282,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA],GSE108436,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues  gut and liver under homesostasis.,parent bioproject:PRJNA427275,pubmed:30386173,,Gut 4 miRNA,GSM2898188,,source name:Gut|tissue:Gut|Sex:male,Gut 4 miRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut 1  Gut 2  Liver 1 and Liver 2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Gut,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,tissue:Gut|Sex:male,GSM2898188,GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq,GSM2898188,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2898188,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127389,,,4.fastq.gz,fastq,643103727.0,12609877.0,GSM2898188 r1,0:51,A:158299708;C:154230134;G:180978224;T:147874496;N:1721165,51,,,,158299708,154230134,180978224,147874496,1721165,SRX3504483,SRS2782037,SRA641250,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.0075,,0.00106,,0.99671,,0.56044,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Adult,Gut,Digestive System
45000,SRR6411467,SRX3504482,SRS2782036,SRP127389,PRJNA427282,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA],GSE108436,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues  gut and liver under homesostasis.,parent bioproject:PRJNA427275,pubmed:30386173,,Gut 3 miRNA,GSM2898187,,source name:Gut|tissue:Gut|Sex:male,Gut 3 miRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut 1  Gut 2  Liver 1 and Liver 2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Gut,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,tissue:Gut|Sex:male,GSM2898187,GSM2898187: Gut 3 miRNA; Danio rerio; miRNA Seq,GSM2898187,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2898187,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127389,,,3.fastq.gz,fastq,657326148.0,12888748.0,GSM2898187 r1,0:51,A:155617794;C:161709285;G:186002579;T:152250836;N:1745654,51,,,,155617794,161709285,186002579,152250836,1745654,SRX3504482,SRS2782036,SRA641250,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.11293,,0.00924,,0.99399,,0.58458,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Adult,Gut,Digestive System
45001,SRR6411466,SRX3504481,SRS2782035,SRP127389,PRJNA427282,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA],GSE108436,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues  gut and liver under homesostasis.,parent bioproject:PRJNA427275,pubmed:30386173,,Liver 2 miRNA,GSM2898186,,source name:Liver|tissue:Liver|Sex:male,Liver 2 miRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut 1  Gut 2  Liver 1 and Liver 2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,,tissue:Liver|Sex:male,GSM2898186,GSM2898186: Liver 2 miRNA; Danio rerio; miRNA Seq,GSM2898186,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA,GEO Accession:GSM2898186,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127389,,,2.fastq.gz,fastq,407289621.0,7986071.0,GSM2898186 r1,0:51,A:84982391;C:104532595;G:122785928;T:93918201;N:1070506,51,,,,84982391,104532595,122785928,93918201,1070506,SRX3504481,SRS2782035,SRA641250,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.13902,,0.01444,,0.99076,,0.58988,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Adult,Liver,Liver and Biliary System