metadata: run_metadata: 59 rows where experiment.library_layout = "SINGLE", experiment.platform = "ION_TORRENT" and tissue_curation

59 rows where experiment.library_layout = "SINGLE", experiment.platform = "ION_TORRENT" and tissue_curation_coarse = "Undetermined"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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.Acount	run.Ccount	run.Gcount	run.Tcount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	ERX604032	ERS557916	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.70048	0.18034	0.88075	0.55658	11	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15551	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	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	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	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	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	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	ERX604027	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.16692	0.04528	0.96384	0.52823	17	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
41420	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	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
41422	41422	SRR4423114	SRX2245298	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							RNA Seq of Zebrafish: Egg pool	99 6	99 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.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534			eggRID0099BC06LargeZF.fastq	fastq	4454090954.0	48098559.0	eggRID0099BC06LargeZF.fastq	0:92.60	A:1084275872;C:1151665265;G:1338679196;T:879470621;N:0	92	1084275872	1151665265	1338679196	879470621	SRX2245298	SRS1745858	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.91346	0.27222	0.96694	0.91118	144	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Undetermined	Undetermined	Undetermined	Undetermined
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	SRX2245296	SRS1745858	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.66115	0.18031	0.89546	0.78468	72	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Undetermined	Undetermined	Undetermined	Undetermined
41426	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	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
59503	59503	SRR11924320	SRX8469993	SRS6770644	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962		PM 3	GSM4591060		source name:protruding mouth stage\|tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	PM 3	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	protruding mouth stage	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591060	GSM4591060: PM 3; Danio rerio; OTHER	GSM4591060		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591060	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951		intentional duplicate	GSE151797_Reference_sequence.fa PM_3.bam	bam bam	215125332.0	6403488.0	GSM4591060 r1	0:33.60	A:50202267;C:65116674;G:52637331;T:47169060;N:0	33	50202267	65116674	52637331	47169060	SRX8469993	SRS6770644	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.73594	0.21617	0.86251	0.68892	42	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Larval	Larval	Undetermined	Undetermined
59504	59504	SRR11924318	SRX8469992	SRS6770643	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962		PM 2	GSM4591059		source name:protruding mouth stage\|tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	PM 2	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	protruding mouth stage	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591059	GSM4591059: PM 2; Danio rerio; OTHER	GSM4591059		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591059	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951		intentional duplicate	GSE151797_Reference_sequence.fa PM_2.bam	bam bam	426315355.0	12915702.0	GSM4591059 r1	0:33.01	A:92276988;C:141702085;G:104175159;T:88161123;N:0	33	92276988	141702085	104175159	88161123	SRX8469992	SRS6770643	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.76385	0.1921	0.87207	0.71495	40	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Larval	Larval	Undetermined	Undetermined
59505	59505	SRR11924317	SRX8469990	SRS6770641	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962		PM 1	GSM4591058		source name:protruding mouth stage\|tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	PM 1	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	protruding mouth stage	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:protruding mouth stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591058	GSM4591058: PM 1; Danio rerio; OTHER	GSM4591058		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591058	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951		intentional duplicate	GSE151797_Reference_sequence.fa PM_1.bam	bam bam	130388595.0	5124384.0	GSM4591058 r1	0:25.44	A:27290253;C:42592303;G:31075292;T:29430747;N:0	25	27290253	42592303	31075292	29430747	SRX8469990	SRS6770641	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.78884	0.23004	0.85113	0.67571	38	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Larval	Larval	Undetermined	Undetermined

Advanced export

JSON shape: default, array, newline-delimited

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");;