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88 rows where experiment.library_strategy = "miRNA-Seq", experiment.platform = "ION_TORRENT" and technology = "unknown"

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tissue_curation 6

devstage_curation_coarse 4

technology 1

  • unknown · 88 ✖

experiment.platform 1

  • ION_TORRENT · 88 ✖

experiment.library_strategy 1

  • miRNA-Seq · 88 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
15550 15550 ERR647595 ERX604031 ERS557915 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 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.       Egg SAMEA2796300 UNIVERSITY OF AMSTERDAM Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1 RID0024 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 RID0024_016.fastq.gz fastq 6684767188.0 89052017.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1 0:75.07 A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0 75       1523328157 1795624453 1849675240 1516139338 0 ERX604031 ERS557915 ERA363845 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.89536   0.15322   0.91421   0.69019   73   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Zygote Embryo Oocyte Reproductive System
15551 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 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 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 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 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 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
41406 41406 SRR4423130 SRX2245314 SRS1745863 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 10 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: prim 16 stage31 hpf 348 10 348 10 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     S10small.fastq fastq 427409571.0 5026564.0 S10small.fastq 0:85.03 A:98026046;C:116630773;G:114413502;T:98339250;N:0 85       98026046 116630773 114413502 98339250 0 SRX2245314 SRS1745863 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.81583   0.17938   0.9094   0.63072   126   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Pharyngula Embryo Embryo Imprecise All anatomical structures
41407 41407 SRR4423129 SRX2245313 SRS1745862 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 9 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 5 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: prim 5 stage24 hpf 348 9 348 9 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     S09small.fastq fastq 516614705.0 6246071.0 S09small.fastq 0:82.71 A:117786535;C:140799134;G:139362428;T:118666608;N:0 82       117786535 140799134 139362428 118666608 0 SRX2245313 SRS1745862 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.81132   0.18952   0.88925   0.69719   17   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Pharyngula Embryo Embryo Imprecise All anatomical structures
41408 41408 SRR4423128 SRX2245312 SRS1745850 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 12 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:protruding mouth stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: protruding mouth stage72 hpf 348 12 348 12 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     S12small.fastq fastq 186817590.0 3062463.0 S12small.fastq 0:61.00 A:42863072;C:49941244;G:49513828;T:44499446;N:0 61       42863072 49941244 49513828 44499446 0 SRX2245312 SRS1745850 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.77668   0.17381   0.8915   0.54189   36   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Larval Larval Embryo Imprecise All anatomical structures
41409 41409 SRR4423127 SRX2245311 SRS1745851 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 11 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:long pec stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: long pec stage48 hpf 348 11 348 11 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     S11small.fastq fastq 405003101.0 5197273.0 S11small.fastq 0:77.93 A:93494059;C:109265919;G:106696649;T:95546474;N:0 77       93494059 109265919 106696649 95546474 0 SRX2245311 SRS1745851 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.78244   0.17047   0.93379   0.6272   30   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Hatching Embryo Embryo Imprecise All anatomical structures
41418 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
41420 41420 SRR4423116 SRX2245300 SRS1745858 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development     egg pools from three different mothers   Egg pool Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Egg pool 94 4 94 4 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     eggRID0094BC04smallZF.fastq fastq 1392075126.0 18333358.0 eggRID0094BC04smallZF.fastq 0:75.93 A:323480979;C:386272283;G:377777594;T:304544270;N:0 75       323480979 386272283 377777594 304544270 0 SRX2245300 SRS1745858 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.68028   0.1685   0.89982   0.84521   83   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Undetermined Undetermined Undetermined Undetermined
41421 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
41424 41424 SRR4423112 SRX2245296 SRS1745858 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development     egg pools from three different mothers   Egg pool Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Egg pool 88 4 88 4 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     eggRID0088BC04smallZF.fastq fastq 1063934659.0 14422089.0 eggRID0088BC04smallZF.fastq 0:73.77 A:248885216;C:293368431;G:288043879;T:233637133;N:0 73       248885216 293368431 288043879 233637133 0 SRX2245296 SRS1745858 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.66115   0.18031   0.89546   0.78468   72   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Undetermined Undetermined Undetermined Undetermined
41425 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
41426 41426 SRR4423110 SRX2245294 SRS1745858 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development     egg pools from three different mothers   Egg pool Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Egg pool 93 4 93 4 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     eggRID0093BC04smallZF.fastq fastq 1382951404.0 18190154.0 eggRID0093BC04smallZF.fastq 0:76.03 A:322536095;C:383176934;G:374216039;T:303022336;N:0 76       322536095 383176934 374216039 303022336 0 SRX2245294 SRS1745858 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.66399   0.17461   0.90134   0.82432   156   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Undetermined Undetermined Undetermined Undetermined
41427 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
41428 41428 SRR4423108 SRX2245292 SRS1745857 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 5 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:90% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 90% epiboly stage 9 hpf 348 5 348 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     S05small.fastq fastq 412237561.0 3386443.0 S05small.fastq 0:121.73 A:91644321;C:118905395;G:115070912;T:86616933;N:0 121       91644321 118905395 115070912 86616933 0 SRX2245292 SRS1745857 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.81233   0.06309   0.93385   0.93973   163   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Gastrula Embryo Embryo Imprecise All anatomical structures
41429 41429 SRR4423107 SRX2245291 SRS1745856 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 6 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 4 somite stage11.3 hpf 348 6 348 6 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     S06small.fastq fastq 535288776.0 4443685.0 S06small.fastq 0:120.46 A:119322177;C:152704452;G:149509408;T:113752739;N:0 120       119322177 152704452 149509408 113752739 0 SRX2245291 SRS1745856 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.82872   0.09035   0.93194   0.81296   159   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Segmentation Embryo Embryo Imprecise All anatomical structures
41430 41430 SRR4423106 SRX2245290 SRS1745854 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 3 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:zfs:0000015 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf 348 3 348 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     S03small.fastq fastq 1025732824.0 7452991.0 S03small.fastq 0:137.63 A:225573059;C:298586545;G:288470386;T:213102834;N:0 137       225573059 298586545 288470386 213102834 0 SRX2245290 SRS1745854 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.8983   0.04271   0.95546   0.91281   159   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Blastula Embryo Embryo Imprecise All anatomical structures
41431 41431 SRR4423105 SRX2245289 SRS1745855 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 4 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:70% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 70% epiboly stage7 hpf 348 4 348 4 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     S04small.fastq fastq 193259658.0 1840126.0 S04small.fastq 0:105.03 A:43516548;C:54669405;G:53501927;T:41571778;N:0 105       43516548 54669405 53501927 41571778 0 SRX2245289 SRS1745855 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.81053   0.16265   0.90698   0.92112   159   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Gastrula Embryo Embryo Imprecise All anatomical structures
41432 41432 SRR4423104 SRX2245288 SRS1745853 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 1 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:64 cells|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 64 cells2 hpf 348 1 348 1 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     S01small.fastq fastq 91910627.0 1396009.0 S01small.fastq 0:65.84 A:21663404;C:25661192;G:25069267;T:19516764;N:0 65       21663404 25661192 25069267 19516764 0 SRX2245288 SRS1745853 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.56828   0.1715   0.92435   0.90047   34   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Cleavage Embryo Embryo Imprecise All anatomical structures
41433 41433 SRR4423103 SRX2245287 SRS1745852 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 2 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:high stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: high stage3.3 hpf 348 2 348 2 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     S02small.fastq fastq 304535574.0 3376105.0 S02small.fastq 0:90.20 A:69193719;C:84372087;G:86707481;T:64262287;N:0 90       69193719 84372087 86707481 64262287 0 SRX2245287 SRS1745852 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.56812   0.09695   0.93474   0.93654   51   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Blastula Embryo Embryo Imprecise All anatomical structures
41436 41436 SRR4423100 SRX2245284 SRS1745849 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 7 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 12 somite stage15 hpf 348 7 348 7 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     S07small.fastq fastq 279201769.0 2713759.0 S07small.fastq 0:102.88 A:61655863;C:78667355;G:77702440;T:61176111;N:0 102       61655863 78667355 77702440 61176111 0 SRX2245284 SRS1745849 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.79087   0.10046   0.89221   0.77892   158   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Segmentation Embryo Embryo Imprecise All anatomical structures
41437 41437 SRR4423099 SRX2245283 SRS1745848 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Time course 8 Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: 22 somite stage20 hpf 348 8 348 8 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     S08small.fastq fastq 520785540.0 4495080.0 S08small.fastq 0:115.86 A:115224831;C:149325753;G:144978190;T:111256766;N:0 115       115224831 149325753 144978190 111256766 0 SRX2245283 SRS1745848 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.83781   0.08976   0.92904   0.80492   183   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Segmentation Embryo Embryo Imprecise All anatomical structures
41457 41457 SRR4449278 SRX2267734 SRS1758938 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S09 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S09 S09 RID0445 S09 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_009_rawlib.basecaller.bam bam 56886794.0 2186951.0 IonXpressRNA 009 rawlib.basecaller.bam 0:26.01 A:15763527;C:12934017;G:13233004;T:14956246;N:0 26       15763527 12934017 13233004 14956246 0 SRX2267734 SRS1758938 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.6501   0.44849   0.83465   0.59625   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-25 Gastrula Embryo Whole Organism All anatomical structures
41458 41458 SRR4449277 SRX2267733 SRS1758937 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S10 RID0445   strain:ABTL|dev stage:51% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S10 S10 RID0445 S10 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_010_rawlib.basecaller.bam bam 63108712.0 2361941.0 IonXpressRNA 010 rawlib.basecaller.bam 0:26.72 A:16956361;C:14496251;G:15049416;T:16606684;N:0 26       16956361 14496251 15049416 16606684 0 SRX2267733 SRS1758937 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.64387   0.42592   0.81091   0.58276   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41459 41459 SRR4449276 SRX2267732 SRS1758936 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S07 RID0445   strain:ABTL|dev stage:47% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S07 S07 RID0445 S07 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_007_rawlib.basecaller.bam bam 50356775.0 1885340.0 IonXpressRNA 007 rawlib.basecaller.bam 0:26.71 A:13603929;C:11508700;G:12096780;T:13147366;N:0 26       13603929 11508700 12096780 13147366 0 SRX2267732 SRS1758936 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63582   0.39586   0.79839   0.56846   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41460 41460 SRR4449275 SRX2267731 SRS1758935 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S08 RID0445   strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S08 S08 RID0445 S08 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_008_rawlib.basecaller.bam bam 63655011.0 2486240.0 IonXpressRNA 008 rawlib.basecaller.bam 0:25.60 A:17274215;C:14286496;G:15277222;T:16817078;N:0 25       17274215 14286496 15277222 16817078 0 SRX2267731 SRS1758935 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.64165   0.41617   0.79931   0.56754   34   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41461 41461 SRR4449274 SRX2267730 SRS1758933 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S05 RID0445   strain:ABTL|dev stage:58% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S05 S05 RID0445 S05 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_005_rawlib.basecaller.bam bam 36352941.0 1403002.0 IonXpressRNA 005 rawlib.basecaller.bam 0:25.91 A:10088289;C:8176923;G:8667822;T:9419907;N:0 25       10088289 8176923 8667822 9419907 0 SRX2267730 SRS1758933 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.59289   0.36407   0.80213   0.57695   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41462 41462 SRR4449273 SRX2267729 SRS1758934 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S06 RID0445   strain:ABTL|dev stage:43% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S06 S06 RID0445 S06 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_006_rawlib.basecaller.bam bam 41157611.0 1592351.0 IonXpressRNA 006 rawlib.basecaller.bam 0:25.85 A:11322629;C:9228187;G:9750979;T:10855816;N:0 25       11322629 9228187 9750979 10855816 0 SRX2267729 SRS1758934 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63095   0.40683   0.8003   0.56985   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41463 41463 SRR4449272 SRX2267728 SRS1758932 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S03 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S03 S03 RID0445 S03 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_003_rawlib.basecaller.bam bam 60356442.0 2057592.0 IonXpressRNA 003 rawlib.basecaller.bam 0:29.33 A:17060096;C:13661341;G:13721228;T:15913777;N:0 29       17060096 13661341 13721228 15913777 0 SRX2267728 SRS1758932 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.73029   0.49935   0.8225   0.56029   30   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41464 41464 SRR4449271 SRX2267727 SRS1758931 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S04 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S04 S04 RID0445 S04 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_004_rawlib.basecaller.bam bam 55705225.0 2055064.0 IonXpressRNA 004 rawlib.basecaller.bam 0:27.11 A:15806355;C:12308008;G:12579212;T:15011650;N:0 27       15806355 12308008 12579212 15011650 0 SRX2267727 SRS1758931 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.70796   0.49815   0.81444   0.54452   41   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41465 41465 SRR4449270 SRX2267726 SRS1758930 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S01 RID0445   strain:ABTL|dev stage:50% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S01 S01 RID0445 S01 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_001_rawlib.basecaller.bam bam 35407241.0 1342552.0 IonXpressRNA 001 rawlib.basecaller.bam 0:26.37 A:9988109;C:7841340;G:8187069;T:9390723;N:0 26       9988109 7841340 8187069 9390723 0 SRX2267726 SRS1758930 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63621   0.43661   0.80992   0.53899   31   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41466 41466 SRR4449269 SRX2267725 SRS1758928 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S02 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S02 S02 RID0445 S02 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_002_rawlib.basecaller.bam bam 40875445.0 1512601.0 IonXpressRNA 002 rawlib.basecaller.bam 0:27.02 A:11593378;C:9124451;G:9444184;T:10713432;N:0 27       11593378 9124451 9444184 10713432 0 SRX2267725 SRS1758928 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.66621   0.45417   0.8127   0.55033   21   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41467 41467 SRR4449267 SRX2267724 SRS1758927 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S15 RID0445   strain:ABTL|dev stage:52% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S15 S15 RID0445 S15 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_015_rawlib.basecaller.bam bam 58421266.0 2091074.0 IonXpressRNA 015 rawlib.basecaller.bam 0:27.94 A:16715618;C:13019609;G:13014639;T:15671400;N:0 27       16715618 13019609 13014639 15671400 0 SRX2267724 SRS1758927 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.71786   0.51457   0.83863   0.53442   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41468 41468 SRR4449266 SRX2267723 SRS1758929 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S16 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S16 S16 RID0445 S16 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_016_rawlib.basecaller.bam bam 55022551.0 2073507.0 IonXpressRNA 016 rawlib.basecaller.bam 0:26.54 A:15319738;C:12288588;G:12653066;T:14761159;N:0 26       15319738 12288588 12653066 14761159 0 SRX2267723 SRS1758929 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.68905   0.46941   0.80306   0.55981   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41469 41469 SRR4449265 SRX2267722 SRS1758926 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S13 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S13 S13 RID0445 S13 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_013_rawlib.basecaller.bam bam 49641484.0 2028008.0 IonXpressRNA 013 rawlib.basecaller.bam 0:24.48 A:13840820;C:11016762;G:11715475;T:13068427;N:0 24       13840820 11016762 11715475 13068427 0 SRX2267722 SRS1758926 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.55355   0.3659   0.81576   0.55987   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41470 41470 SRR4449264 SRX2267721 SRS1758925 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S14 RID0445   strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S14 S14 RID0445 S14 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_014_rawlib.basecaller.bam bam 52969826.0 2019609.0 IonXpressRNA 014 rawlib.basecaller.bam 0:26.23 A:14762618;C:11847782;G:12164393;T:14195033;N:0 26       14762618 11847782 12164393 14195033 0 SRX2267721 SRS1758925 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.65926   0.45113   0.80515   0.56221   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41471 41471 SRR4449263 SRX2267720 SRS1758923 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S11 RID0445   strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S11 S11 RID0445 S11 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_011_rawlib.basecaller.bam bam 54877334.0 2122171.0 IonXpressRNA 011 rawlib.basecaller.bam 0:25.86 A:14884144;C:12539815;G:13173981;T:14279394;N:0 25       14884144 12539815 13173981 14279394 0 SRX2267720 SRS1758923 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.62581   0.40704   0.82002   0.59605   20   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41472 41472 SRR4449262 SRX2267719 SRS1758924 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S12 RID0445   strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S12 S12 RID0445 S12 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_012_rawlib.basecaller.bam bam 51987914.0 1937451.0 IonXpressRNA 012 rawlib.basecaller.bam 0:26.83 A:14499922;C:11778716;G:11957347;T:13751929;N:0 26       14499922 11778716 11957347 13751929 0 SRX2267719 SRS1758924 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.67286   0.44698   0.80919   0.58291   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;