metadata: run_metadata: 224 rows where devstage_curation_coarse = "Adult" and experiment.library

224 rows where devstage_curation_coarse = "Adult" and experiment.library_strategy = "miRNA-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.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	0	ERX701784	ERS659467	ERA410345	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.76262	0.4273	0.8101	0.56676	8	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2015-02-12	Adult	Adult	Undetermined	Undetermined
15505	15505	ERR757153	ERX701783	ERS659466	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Normalization across length	SAMEA3251320	UNIVERSITY OF AMSTERDAM	ENA first public:2015 02 12\|ENA last update:2015 02 12\|External Id:SAMEA3251320\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2015 02 12T17:06:49Z\|INSDC last update:2015 02 12T09:52:20Z\|INSDC status:public\|Submitter Id:Female 002\|common name:zebrafish\|dev stage:Adult\|sample name:Female 002\|sex:female									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2015 02 12\|ENA LAST UPDATE:2018 11 16	RID0035_006.fastq.gz	fastq	193706106.0	6343893.0	ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1	0:30.53	A:52756888;C:42895374;G:46979869;T:51073975;N:0	30		52756888	42895374	46979869	51073975	0	ERX701783	ERS659466	ERA410345	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74991	0.41319	0.83002	0.55823	8	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2015-02-12	Adult	Adult	Undetermined	Undetermined
15506	15506	ERR647638	ERX604074	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_007.fastq.gz	fastq	181485343.0	7581675.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7	0:23.94	A:49408107;C:35660562;G:44520624;T:51896050;N:0	23		49408107	35660562	44520624	51896050	0	ERX604074	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75831	0.16017	0.90723	0.48684	13	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15507	15507	ERR647632	ERX604068	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_001.fastq.gz	fastq	158714692.0	5407747.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1	0:29.35	A:42098161;C:32991434;G:38596553;T:45028544;N:0	29		42098161	32991434	38596553	45028544	0	ERX604068	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75901	0.20293	0.89505	0.48215	24	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15508	15508	ERR647636	ERX604072	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_005.fastq.gz	fastq	124167412.0	4838491.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5	0:25.66	A:33439510;C:24728035;G:30897675;T:35102192;N:0	25		33439510	24728035	30897675	35102192	0	ERX604072	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.76027	0.17783	0.89692	0.48421	30	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15509	15509	ERR647635	ERX604071	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_004.fastq.gz	fastq	124786630.0	4701452.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4	0:26.54	A:33803418;C:24800330;G:30482560;T:35700322;N:0	26		33803418	24800330	30482560	35700322	0	ERX604071	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74872	0.18448	0.89789	0.50377	12	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15510	15510	ERR647634	ERX604070	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_003.fastq.gz	fastq	110526752.0	4078127.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3	0:27.10	A:29453167;C:22981184;G:27444083;T:30648318;N:0	27		29453167	22981184	27444083	30648318	0	ERX604070	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73961	0.1804	0.89686	0.50069	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15511	15511	ERR647633	ERX604069	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_002.fastq.gz	fastq	114721515.0	4468497.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2	0:25.67	A:31387085;C:22123581;G:28270438;T:32940411;N:0	25		31387085	22123581	28270438	32940411	0	ERX604069	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75767	0.17199	0.90118	0.49949	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15512	15512	ERR647645	ERX604081	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_014.fastq.gz	fastq	127742942.0	5487454.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14	0:23.28	A:35700746;C:25577569;G:31187339;T:35277288;N:0	23		35700746	25577569	31187339	35277288	0	ERX604081	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.72451	0.1507	0.91078	0.47283	30	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15513	15513	ERR647644	ERX604080	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_013.fastq.gz	fastq	175319872.0	7193103.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13	0:24.37	A:48008107;C:34657005;G:43047489;T:49607271;N:0	24		48008107	34657005	43047489	49607271	0	ERX604080	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75539	0.16288	0.90388	0.47538	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15514	15514	ERR647643	ERX604079	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_012.fastq.gz	fastq	177443752.0	7567733.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12	0:23.45	A:48143286;C:36300870;G:44060167;T:48939429;N:0	23		48143286	36300870	44060167	48939429	0	ERX604079	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74839	0.15018	0.90782	0.49076	27	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15515	15515	ERR647642	ERX604078	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_011.fastq.gz	fastq	163389373.0	6320373.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11	0:25.85	A:44540588;C:32608476;G:40066295;T:46174014;N:0	25		44540588	32608476	40066295	46174014	0	ERX604078	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75948	0.17375	0.90252	0.47536	33	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15516	15516	ERR647641	ERX604077	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_010.fastq.gz	fastq	128059692.0	5701206.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10	0:22.46	A:35418188;C:24802528;G:31593786;T:36245190;N:0	22		35418188	24802528	31593786	36245190	0	ERX604077	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.72586	0.1331	0.92514	0.4216	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15517	15517	ERR647637	ERX604073	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_006.fastq.gz	fastq	165327404.0	6835740.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 6	0:24.19	A:45252916;C:32442683;G:40306020;T:47325785;N:0	24		45252916	32442683	40306020	47325785	0	ERX604073	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74944	0.16	0.91068	0.47704	21	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15518	15518	ERR647640	ERX604076	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9	RID0015	Reproducibility			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_009.fastq.gz	fastq	134426587.0	5846482.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9	0:22.99	A:36803811;C:26283055;G:33442229;T:37897492;N:0	22		36803811	26283055	33442229	37897492	0	ERX604076	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74219	0.13958	0.91837	0.47819	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15519	15519	ERR647639	ERX604075	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8	RID0015	Fold Change			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0015_008.fastq.gz	fastq	164369360.0	6762174.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8	0:24.31	A:44826982;C:33030972;G:40615427;T:45895979;N:0	24		44826982	33030972	40615427	45895979	0	ERX604075	ERS557914	ERA363852	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75513	0.16254	0.90534	0.50535	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15520	15520	ERR647623	ERX604059	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_008.fastq.gz	fastq	198146766.0	7373392.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8	0:26.87	A:50518864;C:42346985;G:50683068;T:54597849;N:0	26		50518864	42346985	50683068	54597849	0	ERX604059	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73719	0.16567	0.89869	0.49695	76	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15521	15521	ERR647622	ERX604058	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_007.fastq.gz	fastq	240260456.0	9194064.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7	0:26.13	A:62434032;C:50861577;G:60916218;T:66048629;N:0	26		62434032	50861577	60916218	66048629	0	ERX604058	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73042	0.17017	0.89509	0.51784	44	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15522	15522	ERR647620	ERX604056	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_005.fastq.gz	fastq	140470735.0	4903805.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5	0:28.65	A:35312706;C:29191443;G:36788541;T:39178045;N:0	28		35312706	29191443	36788541	39178045	0	ERX604056	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.76081	0.16609	0.90216	0.48155	72	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15523	15523	ERR647617	ERX604053	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_002.fastq.gz	fastq	113953599.0	4875815.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2	0:23.37	A:29576305;C:23096908;G:29656780;T:31623606;N:0	23		29576305	23096908	29656780	31623606	0	ERX604053	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.70891	0.13528	0.91208	0.4622	24	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15524	15524	ERR647624	ERX604060	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_009.fastq.gz	fastq	127769435.0	5492615.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9	0:23.26	A:34397217;C:25332113;G:31991788;T:36048317;N:0	23		34397217	25332113	31991788	36048317	0	ERX604060	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.71147	0.1472	0.91015	0.49014	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15525	15525	ERR647629	ERX604065	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_014.fastq.gz	fastq	83983757.0	3823842.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14	0:21.96	A:22501534;C:16455147;G:21619305;T:23407771;N:0	21		22501534	16455147	21619305	23407771	0	ERX604065	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.70211	0.13351	0.92038	0.45898	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15526	15526	ERR647631	ERX604067	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_016.fastq.gz	fastq	117220472.0	4272650.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16	0:27.44	A:29509123;C:25768315;G:30220006;T:31723028;N:0	27		29509123	25768315	30220006	31723028	0	ERX604067	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.68585	0.14679	0.90778	0.49492	20	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15527	15527	ERR647618	ERX604054	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_003.fastq.gz	fastq	165279016.0	5211580.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3	0:31.71	A:41451579;C:36699133;G:41477197;T:45651107;N:0	31		41451579	36699133	41477197	45651107	0	ERX604054	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.71827	0.17456	0.90554	0.50274	18	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15528	15528	ERR647621	ERX604057	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_006.fastq.gz	fastq	181164500.0	7686285.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6	0:23.57	A:48622049;C:36019225;G:45318073;T:51205153;N:0	23		48622049	36019225	45318073	51205153	0	ERX604057	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73267	0.15948	0.9026	0.483	14	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15529	15529	ERR647619	ERX604055	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_004.fastq.gz	fastq	131702671.0	4688094.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4	0:28.09	A:32537215;C:28853793;G:34317576;T:35994087;N:0	28		32537215	28853793	34317576	35994087	0	ERX604055	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.68635	0.14911	0.90532	0.50027	31	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15530	15530	ERR647628	ERX604064	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_013.fastq.gz	fastq	123881257.0	5143681.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13	0:24.08	A:32852368;C:25503683;G:31339781;T:34185425;N:0	24		32852368	25503683	31339781	34185425	0	ERX604064	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.72384	0.15147	0.90648	0.46	24	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15531	15531	ERR647627	ERX604063	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_012.fastq.gz	fastq	135155439.0	6123293.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12	0:22.07	A:35870227;C:27070386;G:34401412;T:37813414;N:0	22		35870227	27070386	34401412	37813414	0	ERX604063	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.69126	0.12647	0.91695	0.46572	25	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15532	15532	ERR647626	ERX604062	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_011.fastq.gz	fastq	138836612.0	5648801.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11	0:24.58	A:36426455;C:28359755;G:34985736;T:39064666;N:0	24		36426455	28359755	34985736	39064666	0	ERX604062	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73565	0.15718	0.90382	0.45772	67	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15533	15533	ERR647625	ERX604061	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_010.fastq.gz	fastq	182404716.0	6612019.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10	0:27.59	A:47718609;C:38775928;G:45637186;T:50272993;N:0	27		47718609	38775928	45637186	50272993	0	ERX604061	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75246	0.19746	0.88544	0.48212	36	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15534	15534	ERR647616	ERX604052	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:086 1	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_001.fastq.gz	fastq	137653436.0	5155975.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 1	0:26.70	A:34561717;C:29961559;G:35320222;T:37809938;N:0	26		34561717	29961559	35320222	37809938	0	ERX604052	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.71887	0.15223	0.90824	0.49462	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15535	15535	ERR647630	ERX604066	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15	RID0017	EtOH conc. experiment			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0017_015.fastq.gz	fastq	101714594.0	4045987.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15	0:25.14	A:26518632;C:20741074;G:25853629;T:28601259;N:0	25		26518632	20741074	25853629	28601259	0	ERX604066	ERS557914	ERA363851	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74566	0.16455	0.89534	0.48977	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15536	15536	ERR647610	ERX604046	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent PGM sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM		ERP007147	Ion Torrent PGM sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_009.fastq.gz	fastq	114880508.0	4321457.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1	0:26.58	A:31499097;C:23030789;G:27803371;T:32547251;N:0	26		31499097	23030789	27803371	32547251	0	ERX604046	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.7932	0.2086	0.89045	0.49364	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15537	15537	ERR647611	ERX604047	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_010.fastq.gz	fastq	124380158.0	4885304.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2	0:25.46	A:33809369;C:25116497;G:30529372;T:34924920;N:0	25		33809369	25116497	30529372	34924920	0	ERX604047	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.78302	0.1944	0.89398	0.50469	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15538	15538	ERR647612	ERX604048	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_011.fastq.gz	fastq	122081664.0	4959591.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3	0:24.62	A:33452935;C:24151113;G:29942213;T:34535403;N:0	24		33452935	24151113	29942213	34535403	0	ERX604048	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.77425	0.18982	0.8911	0.46046	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15539	15539	ERR647615	ERX604051	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_014.fastq.gz	fastq	120491210.0	4564333.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6	0:26.40	A:33116448;C:24416657;G:29447901;T:33510204;N:0	26		33116448	24416657	29447901	33510204	0	ERX604051	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.77843	0.20568	0.88605	0.51892	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15540	15540	ERR647614	ERX604050	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_013.fastq.gz	fastq	108193052.0	4221217.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5	0:25.63	A:29795112;C:21481151;G:26281164;T:30635625;N:0	25		29795112	21481151	26281164	30635625	0	ERX604050	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.78861	0.19966	0.89207	0.49332	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15541	15541	ERR647613	ERX604049	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4	RID0023	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0023_012.fastq.gz	fastq	134807115.0	5232713.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4	0:25.76	A:37141537;C:27086121;G:32486547;T:38092910;N:0	25		37141537	27086121	32486547	38092910	0	ERX604049	ERS557914	ERA363850	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.78328	0.20061	0.88903	0.51655	32	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15542	15542	ERR647603	ERX604039	ERS557923	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Female 016	SAMEA2796308	UNIVERSITY OF AMSTERDAM	Alias:Female 016\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:25Z\|INSDC status:public\|SRA accession:ERS557923\|Sample Name:ERS557923\|Title:Male vs Female\|dev stage:Adult\|sex:female\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_010.fastq.gz	fastq	186445198.0	6054478.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8	0:30.79	A:51431122;C:41043403;G:44213690;T:49756983;N:0	30		51431122	41043403	44213690	49756983	0	ERX604039	ERS557923	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74649	0.44738	0.84254	0.55199	13	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15543	15543	ERR647602	ERX604038	ERS557922	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Female 014	SAMEA2796307	UNIVERSITY OF AMSTERDAM	Alias:Female 014\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:25Z\|INSDC status:public\|SRA accession:ERS557922\|Sample Name:ERS557922\|Title:Male vs Female\|dev stage:Adult\|sex:female\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_009.fastq.gz	fastq	199860614.0	6227225.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7	0:32.09	A:53999848;C:44698032;G:48251471;T:52911263;N:0	32		53999848	44698032	48251471	52911263	0	ERX604038	ERS557922	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.75262	0.42794	0.83619	0.5624	29	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15544	15544	ERR647601	ERX604037	ERS557921	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Female 008	SAMEA2796306	UNIVERSITY OF AMSTERDAM	Alias:Female 008\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:25Z\|INSDC status:public\|SRA accession:ERS557921\|Sample Name:ERS557921\|Title:Male vs Female\|dev stage:Adult\|sex:female\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_008.fastq.gz	fastq	190251948.0	6082600.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6	0:31.28	A:50176174;C:43027879;G:47458847;T:49589048;N:0	31		50176174	43027879	47458847	49589048	0	ERX604037	ERS557921	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.72654	0.373	0.82785	0.52436	25	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15545	15545	ERR647600	ERX604036	ERS557920	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Female 007	SAMEA2796305	UNIVERSITY OF AMSTERDAM	Alias:Female 007\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:24Z\|INSDC status:public\|SRA accession:ERS557920\|Sample Name:ERS557920\|Title:Male vs Female\|dev stage:Adult\|sex:female\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_007.fastq.gz	fastq	214503694.0	6990446.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5	0:30.69	A:59354819;C:47472262;G:51306173;T:56370440;N:0	30		59354819	47472262	51306173	56370440	0	ERX604036	ERS557920	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74272	0.45587	0.83161	0.53444	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15546	15546	ERR647599	ERX604035	ERS557919	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 014	SAMEA2796304	UNIVERSITY OF AMSTERDAM	Alias:Male 014\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:24Z\|INSDC status:public\|SRA accession:ERS557919\|Sample Name:ERS557919\|Title:Male vs Female\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_005.fastq.gz	fastq	235098531.0	7522781.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4	0:31.25	A:58178492;C:54009752;G:64159987;T:58750300;N:0	31		58178492	54009752	64159987	58750300	0	ERX604035	ERS557919	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.73752	0.19698	0.86665	0.58697	13	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15547	15547	ERR647598	ERX604034	ERS557918	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 011	SAMEA2796303	UNIVERSITY OF AMSTERDAM	Alias:Male 011\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:24Z\|INSDC status:public\|SRA accession:ERS557918\|Sample Name:ERS557918\|Title:Male vs Female\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_004.fastq.gz	fastq	223142261.0	6553993.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3	0:34.05	A:55488952;C:50941034;G:58123716;T:58588559;N:0	34		55488952	50941034	58123716	58588559	0	ERX604034	ERS557918	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.74686	0.2139	0.86996	0.55375	11	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15548	15548	ERR647597	ERX604033	ERS557917	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 006	SAMEA2796302	UNIVERSITY OF AMSTERDAM	Alias:Male 006\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:24Z\|INSDC status:public\|SRA accession:ERS557917\|Sample Name:ERS557917\|Title:Male vs Female\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_002.fastq.gz	fastq	166401146.0	5656405.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2	0:29.42	A:41137490;C:38824883;G:44865980;T:41572793;N:0	29		41137490	38824883	44865980	41572793	0	ERX604033	ERS557917	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.69452	0.18245	0.87044	0.58162	11	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15549	15549	ERR647596	ERX604032	ERS557916	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 003	SAMEA2796301	UNIVERSITY OF AMSTERDAM	Alias:Male 003\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:38:23Z\|INSDC status:public\|SRA accession:ERS557916\|Sample Name:ERS557916\|Title:Male vs Female\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1	RID0035	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0035_001.fastq.gz	fastq	167146177.0	6380638.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1	0:26.20	A:43620211;C:36811253;G:43301042;T:43413671;N:0	26		43620211	36811253	43301042	43413671	0	ERX604032	ERS557916	ERA363846	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.70048	0.18034	0.88075	0.55658	11	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15551	15551	ERR647594	ERX604030	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_015.fastq.gz	fastq	273349184.0	9019669.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6	0:30.31	A:74069549;C:59041449;G:64551451;T:75686735;N:0	30		74069549	59041449	64551451	75686735	0	ERX604030	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.78759	0.26081	0.90989	0.51416	29	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15552	15552	ERR647589	ERX604025	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_010.fastq.gz	fastq	54651692.0	2000589.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1	0:27.32	A:16624629;C:13894132;G:10557585;T:13575346;N:0	27		16624629	13894132	10557585	13575346	0	ERX604025	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.11072	0.02655	0.97749	0.53916	26	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15553	15553	ERR647590	ERX604026	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_011.fastq.gz	fastq	47051190.0	1414933.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2	0:33.25	A:12984359;C:11329853;G:10330928;T:12406050;N:0	33		12984359	11329853	10330928	12406050	0	ERX604026	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.36871	0.10094	0.9483	0.51008	40	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15554	15554	ERR647592	ERX604028	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_013.fastq.gz	fastq	394812059.0	13329274.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4	0:29.62	A:108705027;C:84131955;G:92090437;T:109884640;N:0	29		108705027	84131955	92090437	109884640	0	ERX604028	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.65205	0.21183	0.91977	0.52643	21	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15555	15555	ERR647593	ERX604029	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_014.fastq.gz	fastq	143238806.0	4225461.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5	0:33.90	A:38374880;C:31424768;G:33687670;T:39751488;N:0	33		38374880	31424768	33687670	39751488	0	ERX604029	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.78469	0.26587	0.92178	0.51694	80	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
15556	15556	ERR647591	ERX604027	ERS557914	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Male 001	SAMEA2796299	UNIVERSITY OF AMSTERDAM	Alias:Male 001\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:42:44Z\|INSDC status:public\|SRA accession:ERS557914\|Sample Name:ERS557914\|Title:Male ZF\|dev stage:Adult\|sex:male\|strain:ABxTL									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3	RID0011	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0011_012.fastq.gz	fastq	55541174.0	1649692.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3	0:33.67	A:16076639;C:14164415;G:11139997;T:14160123;N:0	33		16076639	14164415	11139997	14160123	0	ERX604027	ERS557914	ERA363842	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.16692	0.04528	0.96384	0.52823	17	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Adult	Adult	Undetermined	Undetermined
36560	36560	SRR1048073	SRX363298	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.			Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland											Zebrafish Brain miRNA	Brain miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132			ZB_trimmed.fastq	fastq	323899236.0	14781569.0	Brain miRNA run	0:21.91 1:0	A:77705253;C:63882329;G:85902986;T:96383552;N:25116	21	0	77705253	63882329	85902986	96383552	25116	SRX363298	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.88754	0.06569	0.96747	0.53358	23	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
36561	36561	SRR1048072	SRX363297	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.			Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland											Zebrafish pineal gland dark miRNA	Pineal gland dark miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132			D_trimmed.fastq	fastq	231371620.0	10385264.0	Pineal gland dark miRNA run	0:22.28 1:0	A:61228408;C:44264639;G:58700027;T:67159878;N:18668	22	0	61228408	44264639	58700027	67159878	18668	SRX363297	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.84648	0.04467	0.95645	0.79978	22	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
36562	36562	SRR1048071	SRX363296	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.			Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland											Zebrafish pineal gland light miRNA	Pineal gland light miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132			L_trimmed.fastq	fastq	132417471.0	5933638.0	Pineal gland light miRNA run	0:22.32 1:0	A:36017069;C:26569684;G:32546616;T:37273526;N:10576	22	0	36017069	26569684	32546616	37273526	10576	SRX363296	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.86427	0.03426	0.95631	0.86509	21	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
37921	37921	SRR1554495	SRX685396	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary2	ZF4Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_3.fq.gz	fastq	1225610154.0	12134754.0	Ovary2 Run3	0:101	A:347141358;C:303255805;G:280185540;T:294456010;N:571441	101		347141358	303255805	280185540	294456010	571441	SRX685396	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	1e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37922	37922	SRR1554492	SRX685395	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis2	ZF2Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_3.fq.gz	fastq	1192024422.0	11802222.0	Testis2 Run3	0:101	A:373380865;C:276125943;G:251033102;T:290931637;N:552875	101		373380865	276125943	251033102	290931637	552875	SRX685395	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	1e-05	0.99997	0.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37923	37923	SRR1554489	SRX685394	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Heart2	ZF2Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_3.fq.gz	fastq	1302765670.0	12898670.0	Heart2 Run3	0:101	A:397689061;C:312745449;G:268626802;T:323141419;N:562939	101		397689061	312745449	268626802	323141419	562939	SRX685394	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	2e-05	0.99997	1.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37924	37924	SRR1554486	SRX685392	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain2	ZF2Brain2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_3.fq.gz	fastq	1211892536.0	11998936.0	Brain2 Run3	0:101	A:374228993;C:286134640;G:253944548;T:297038575;N:545780	101		374228993	286134640	253944548	297038575	545780	SRX685392	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37925	37925	SRR1554483	SRX685391	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary1	ZF3Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_3.fq.gz	fastq	347516154.0	3440754.0	Ovary1 Run3	0:101	A:107805981;C:80183725;G:73617313;T:85763181;N:145954	101		107805981	80183725	73617313	85763181	145954	SRX685391	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05	4e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37926	37926	SRR1554480	SRX685390	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis1	ZF1Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_3.fq.gz	fastq	1184228636.0	11725036.0	Testis1 Run3	0:101	A:340636900;C:278505979;G:259975802;T:304564724;N:545231	101		340636900	278505979	259975802	304564724	545231	SRX685390	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	1e-05	0.0	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37927	37927	SRR1554477	SRX685389	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish individual 1 heart	ZF1Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_3.fq.gz	fastq	1561371524.0	15459124.0	Heart1 Run3	0:101	A:454757966;C:391143691;G:334715236;T:380114024;N:640607	101		454757966	391143691	334715236	380114024	640607	SRX685389	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	2e-05	0.99997	1.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37928	37928	SRR1554474	SRX685388	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain1	ZFBrain1 2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_3.fq.gz	fastq	1192445794.0	11806394.0	Brain1 Run3	0:101	A:369786121;C:268557682;G:265557417;T:288006805;N:537769	101		369786121	268557682	265557417	288006805	537769	SRX685388	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	1e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37929	37929	SRR1554493	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_1.fq.gz	fastq	476104278.0	9335378.0	Ovary2 Run1	0:51	A:111060704;C:120863975;G:129849761;T:114224677;N:105161	51		111060704	120863975	129849761	114224677	105161	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00027	8e-05	0.99945	0.8125	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37930	37930	SRR1554494	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_2.fq.gz	fastq	561956352.0	11018752.0	Ovary2 Run2	0:51	A:129925815;C:148479658;G:148478706;T:132824290;N:2247883	51		129925815	148479658	148478706	132824290	2247883	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022	0.0001	0.99967	0.6875	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37931	37931	SRR1554490	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_1.fq.gz	fastq	586152231.0	11493181.0	Testis2 Run1	0:51	A:145360493;C:148943988;G:151402108;T:140286245;N:159397	51		145360493	148943988	151402108	140286245	159397	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05	2e-05	0.99985	0.57142	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37932	37932	SRR1554491	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_2.fq.gz	fastq	697016337.0	13666987.0	Testis2 Run2	0:51	A:172082858;C:184634425;G:173370430;T:163527914;N:3400710	51		172082858	184634425	173370430	163527914	3400710	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05	2e-05	0.99985	0.57142	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37933	37933	SRR1554487	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_1.fq.gz	fastq	767836212.0	15055612.0	Heart2 Run1	0:51	A:192620363;C:202013249;G:191038597;T:181862075;N:301928	51		192620363	202013249	191038597	181862075	301928	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05	3e-05	0.99995	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37934	37934	SRR1554488	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_2.fq.gz	fastq	979886205.0	19213455.0	Heart2 Run2	0:51	A:246169086;C:264387065;G:236377487;T:227289693;N:5662874	51		246169086	264387065	236377487	227289693	5662874	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37935	37935	SRR1554484	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_1.fq.gz	fastq	654412671.0	12831621.0	Brain2 Run1	0:51	A:160544180;C:166355290;G:168608762;T:158684308;N:220131	51		160544180	166355290	168608762	158684308	220131	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	0.0	0.99993	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37936	37936	SRR1554485	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_2.fq.gz	fastq	856322793.0	16790643.0	Brain2 Run2	0:51	A:210706815;C:226772546;G:212404752;T:201722093;N:4716587	51		210706815	226772546	212404752	201722093	4716587	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37937	37937	SRR1554481	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_1.fq.gz	fastq	116086965.0	2276215.0	Ovary1 Run1	0:51	A:29237121;C:30235277;G:29264328;T:27320814;N:29425	51		29237121	30235277	29264328	27320814	29425	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022	9e-05	0.99967	0.65	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37938	37938	SRR1554482	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_2.fq.gz	fastq	138905844.0	2723644.0	Ovary1 Run2	0:51	A:34695180;C:38015933;G:33434207;T:32057083;N:703441	51		34695180	38015933	33434207	32057083	703441	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00016	5e-05	0.99977	0.42857	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37939	37939	SRR1554478	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_1.fq.gz	fastq	655515750.0	12853250.0	Testis1 Run1	0:51	A:152422885;C:163771947;G:179144090;T:159997538;N:179290	51		152422885	163771947	179144090	159997538	179290	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0011	0.00053	0.99829	0.67777	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37940	37940	SRR1554479	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_2.fq.gz	fastq	777594399.0	15246949.0	Testis1 Run2	0:51	A:180116528;C:202508153;G:204833105;T:186435696;N:3700917	51		180116528	202508153	204833105	186435696	3700917	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00073	0.00032	0.99898	0.62745	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37941	37941	SRR1554475	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_1.fq.gz	fastq	810162642.0	15885542.0	Heart1 Run1	0:51	A:199665102;C:213941735;G:204361738;T:191870055;N:324012	51		199665102	213941735	204361738	191870055	324012	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	6e-05	1e-05	0.99989	0.8	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37942	37942	SRR1554476	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_2.fq.gz	fastq	1013563698.0	19873798.0	Heart1 Run2	0:51	A:249913434;C:275453651;G:247166233;T:235034199;N:5996181	51		249913434	275453651	247166233	235034199	5996181	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	4e-05	2e-05	0.99997	0.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37943	37943	SRR1554472	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_1.fq.gz	fastq	679860294.0	13330594.0	Brain1 Run1	0:51	A:167202435;C:176450132;G:174468721;T:161497185;N:241821	51		167202435	176450132	174468721	161497185	241821	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37944	37944	SRR1554473	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal									Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_2.fq.gz	fastq	838372782.0	16438682.0	Brain1 Run2	0:51	A:206906228;C:221202670;G:210716690;T:195319694;N:4227500	51		206906228	221202670	210716690	195319694	4227500	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
38046	38046	SRR1427469	SRX612649	SRS643610	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		28d	GSM1417152		source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	28d	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417152	GSM1417152: 28d; Danio rerio; miRNA Seq	GSM1417152		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417152	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465			28d.fq	bam	694299184.0	32089203.0	GSM1417152 r1	0:21.64 1:0	A:174747494;C:132129648;G:193085254;T:194336788;N:0	21	0	174747494	132129648	193085254	194336788	0	SRX612649	SRS643610	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93434	0.05272	0.98831	0.56642	23	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38047	38047	SRR1427468	SRX612648	SRS643609	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		72h	GSM1417151		source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	72h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417151	GSM1417151: 72h; Danio rerio; miRNA Seq	GSM1417151		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417151	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465			72h.fq	fastq	689263089.0	31419317.0	GSM1417151 r1	0:21.94 1:0	A:161567060;C:125003691;G:193763870;T:208928468;N:0	21	0	161567060	125003691	193763870	208928468	0	SRX612648	SRS643609	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93237	0.03751	0.98774	0.51765	20	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38048	38048	SRR1427467	SRX612647	SRS643608	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		0h	GSM1417150		source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	0h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417150	GSM1417150: 0h; Danio rerio; miRNA Seq	GSM1417150		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417150	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465			0h.bam	fastq	3005859202.0	134278309.0	GSM1417150 r1	0:22.39	A:762111385;C:628084257;G:836553469;T:779110091;N:0	22		762111385	628084257	836553469	779110091	0	SRX612647	SRS643608	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.94362	0.03903	0.99093	0.5848	22	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
39609	39609	SRR1873571	SRX915251	SRS870223	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		fins	GSM1630515		source name:adult fins 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:fins\|developmental stage:adult\|age:1 year	fins	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult fins 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:fins\|developmental stage:adult\|age:1 year	GSM1630515	GSM1630515: fins; Danio rerio; miRNA Seq	GSM1630515		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630515	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					113161.0	2108.0	GSM1630515 r1	0:4 1:49.68	A:30303;C:30710;G:27210;T:24785;N:153	4	49	30303	30710	27210	24785	153	SRX915251	SRS870223	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		50	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Fin	Surface Structure
39610	39610	SRR1873570	SRX915250	SRS870224	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		skin	GSM1630514		source name:adult skin 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:skin\|developmental stage:adult\|age:1 year	skin	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult skin 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:skin\|developmental stage:adult\|age:1 year	GSM1630514	GSM1630514: skin; Danio rerio; miRNA Seq	GSM1630514		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630514	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					79232.0	1527.0	GSM1630514 r1	0:4 1:47.89	A:20622;C:23508;G:19017;T:15967;N:118	4	47	20622	23508	19017	15967	118	SRX915250	SRS870224	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		53	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Skin	Surface Structure
39611	39611	SRR1873569	SRX915249	SRS870225	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		heart	GSM1630513		source name:adult heart 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:heart\|developmental stage:adult\|age:1 year	heart	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult heart 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:heart\|developmental stage:adult\|age:1 year	GSM1630513	GSM1630513: heart; Danio rerio; miRNA Seq	GSM1630513		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630513	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					39500.0	711.0	GSM1630513 r1	0:4 1:51.56	A:11300;C:9125;G:9195;T:9835;N:45	4	51	11300	9125	9195	9835	45	SRX915249	SRS870225	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		53	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Heart	Cardiovascular System
39612	39612	SRR1873568	SRX915248	SRS870226	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		gills	GSM1630512		source name:adult gills 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:gills\|developmental stage:adult\|age:1 year	gills	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult gills 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:gills\|developmental stage:adult\|age:1 year	GSM1630512	GSM1630512: gills; Danio rerio; miRNA Seq	GSM1630512		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630512	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					189248.0	3563.0	GSM1630512 r1	0:4 1:49.11	A:48212;C:55198;G:44765;T:40711;N:362	4	49	48212	55198	44765	40711	362	SRX915248	SRS870226	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		44	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Gill	Respiratory System
39613	39613	SRR1873567	SRX915247	SRS870227	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		eyes	GSM1630511		source name:adult eyes 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:eyes\|developmental stage:adult\|age:1 year	eyes	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult eyes 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:eyes\|developmental stage:adult\|age:1 year	GSM1630511	GSM1630511: eyes; Danio rerio; miRNA Seq	GSM1630511		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630511	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					173069.0	3135.0	GSM1630511 r1	0:4 1:51.21	A:50732;C:44705;G:40960;T:36324;N:348	4	51	50732	44705	40960	36324	348	SRX915247	SRS870227	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		52	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Eye	Sensory System
39614	39614	SRR1873566	SRX915246	SRS870228	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		brain	GSM1630510		source name:adult brain 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:brain\|developmental stage:adult\|age:1 year	brain	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult brain 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:brain\|developmental stage:adult\|age:1 year	GSM1630510	GSM1630510: brain; Danio rerio; miRNA Seq	GSM1630510		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630510	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					688279.0	12620.0	GSM1630510 r1	0:4 1:50.54	A:205782;C:180028;G:171745;T:129693;N:1031	4	50	205782	180028	171745	129693	1031	SRX915246	SRS870228	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		48	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Brain	Nervous System
39615	39615	SRR1873565	SRX915245	SRS870229	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		adult	GSM1630509		source name:entire adult\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:adult\|age:1 year	adult	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	entire adult		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:adult\|age:1 year	GSM1630509	GSM1630509: adult; Danio rerio; miRNA Seq	GSM1630509		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630509	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014					361024.0	6498.0	GSM1630509 r1	0:4 1:51.56	A:104704;C:84406;G:83224;T:87843;N:847	4	51	104704	84406	83224	87843	847	SRX915245	SRS870229	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Trunk	Surface Structure
41418	41418	SRR4423118	SRX2245302	SRS1745860	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development					Adult FT Dr		strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:female\|tissue:tail\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: Adult female tail	172 5	172 5	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534			femaletailRID0172BC05smallZF.fastq	fastq	491055734.0	7690105.0	femaletailRID0172BC05smallZF.fastq	0:63.86	A:114732043;C:132287469;G:130972143;T:113064079;N:0	63		114732043	132287469	130972143	113064079	0	SRX2245302	SRS1745860	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.82246	0.13521	0.91303	0.63226	43	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Tail	Multi-system
41421	41421	SRR4423115	SRX2245299	SRS1745859	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development					Adult MWB Dr		strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:male\|tissue:whole body\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: Adult male whole body	94 3	94 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534			maleRID0094BC03smallZF.fastq	fastq	697814234.0	14408051.0	maleRID0094BC03smallZF.fastq	0:48.43	A:165337411;C:177790468;G:184204311;T:170482044;N:0	48		165337411	177790468	184204311	170482044	0	SRX2245299	SRS1745859	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.70426	0.16215	0.91027	0.5459	120	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Trunk	Surface Structure
41425	41425	SRR4423111	SRX2245295	SRS1745859	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development					Adult MWB Dr		strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:male\|tissue:whole body\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: Adult male whole body	88 3	88 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534			maleRID0088BC03smallZF.fastq	fastq	523776538.0	11118832.0	maleRID0088BC03smallZF.fastq	0:47.11	A:123827431;C:133478804;G:138882662;T:127587641;N:0	47		123827431	133478804	138882662	127587641	0	SRX2245295	SRS1745859	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.69556	0.16368	0.9093	0.54838	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Trunk	Surface Structure
41427	41427	SRR4423109	SRX2245293	SRS1745859	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development					Adult MWB Dr		strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:male\|tissue:whole body\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: Adult male whole body	93 3	93 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534			maleRID0093BC03smallZF.fastq	fastq	692750598.0	14286031.0	maleRID0093BC03smallZF.fastq	0:48.49	A:164412063;C:176380331;G:182539801;T:169418403;N:0	48		164412063	176380331	182539801	169418403	0	SRX2245293	SRS1745859	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.70738	0.16645	0.90948	0.55306	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Trunk	Surface Structure
43050	43050	SRR5883565	SRX3049654	SRS2396336	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver BPA 4 6	GSM2722577		tissue:Liver\|exposure:100 nM BPA	Liver BPA 4 6	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:100 nM BPA	GSM2722577	GSM2722577: Liver BPA 4 6; Danio rerio; miRNA Seq	GSM2722577		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722577	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397			12_GGTAGC_LALL_R1_001.fastq.gz	fastq	461508486.0	9049186.0	GSM2722577 r1	0:51	A:92718489;C:120118265;G:143926288;T:103539215;N:1206229	51		92718489	120118265	143926288	103539215	1206229	SRX3049654	SRS2396336	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.02792	0.00247	0.99602	0.60254	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43051	43051	SRR5883564	SRX3049653	SRS2396335	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver BPA 1 3	GSM2722576		tissue:Liver\|exposure:100 nM BPA	Liver BPA 1 3	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:100 nM BPA	GSM2722576	GSM2722576: Liver BPA 1 3; Danio rerio; miRNA Seq	GSM2722576		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722576	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397			11_GAGTGG_LALL_R1_001.fastq.gz	fastq	587697684.0	11523484.0	GSM2722576 r1	0:51	A:131489823;C:140167421;G:171253226;T:143217998;N:1569216	51		131489823	140167421	171253226	143217998	1569216	SRX3049653	SRS2396335	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.03603	0.00774	0.98492	0.65361	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43052	43052	SRR5883563	SRX3049652	SRS2396334	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver CNTRL 4 5	GSM2722575		tissue:Liver\|exposure:Control	Liver CNTRL 4 5	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:Control	GSM2722575	GSM2722575: Liver CNTRL 4 5; Danio rerio; miRNA Seq	GSM2722575		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722575	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397			10_CGTACG_LALL_R1_001.fastq.gz	fastq	407289621.0	7986071.0	GSM2722575 r1	0:51	A:84982391;C:104532595;G:122785928;T:93918201;N:1070506	51		84982391	104532595	122785928	93918201	1070506	SRX3049652	SRS2396334	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.13902	0.01445	0.99086	0.57915	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43053	43053	SRR5883562	SRX3049651	SRS2396333	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver CNTRL 1 3	GSM2722574		tissue:Liver\|exposure:Control	Liver CNTRL 1 3	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:Control	GSM2722574	GSM2722574: Liver CNTRL 1 3; Danio rerio; miRNA Seq	GSM2722574		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722574	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397			9_GTTTCG_LALL_R1_001.fastq.gz	fastq	379997073.0	7450923.0	GSM2722574 r1	0:51	A:79538003;C:96525448;G:113901755;T:89020494;N:1011373	51		79538003	96525448	113901755	89020494	1011373	SRX3049651	SRS2396333	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.00447	0.0005	0.99626	0.57217	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
44999	44999	SRR6411468	SRX3504483	SRS2782037	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Gut 4 miRNA	GSM2898188		source name:Gut\|tissue:Gut\|Sex:male	Gut 4 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Gut	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Gut\|Sex:male	GSM2898188	GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq	GSM2898188		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898188	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389			4.fastq.gz	fastq	643103727.0	12609877.0	GSM2898188 r1	0:51	A:158299708;C:154230134;G:180978224;T:147874496;N:1721165	51		158299708	154230134	180978224	147874496	1721165	SRX3504483	SRS2782037	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.0075	0.00106	0.99671	0.56044	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Gut	Digestive System
45000	45000	SRR6411467	SRX3504482	SRS2782036	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Gut 3 miRNA	GSM2898187		source name:Gut\|tissue:Gut\|Sex:male	Gut 3 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Gut	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Gut\|Sex:male	GSM2898187	GSM2898187: Gut 3 miRNA; Danio rerio; miRNA Seq	GSM2898187		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898187	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389			3.fastq.gz	fastq	657326148.0	12888748.0	GSM2898187 r1	0:51	A:155617794;C:161709285;G:186002579;T:152250836;N:1745654	51		155617794	161709285	186002579	152250836	1745654	SRX3504482	SRS2782036	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.11293	0.00924	0.99399	0.58458	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Gut	Digestive System
45001	45001	SRR6411466	SRX3504481	SRS2782035	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Liver 2 miRNA	GSM2898186		source name:Liver\|tissue:Liver\|Sex:male	Liver 2 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Liver\|Sex:male	GSM2898186	GSM2898186: Liver 2 miRNA; Danio rerio; miRNA Seq	GSM2898186		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898186	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389			2.fastq.gz	fastq	407289621.0	7986071.0	GSM2898186 r1	0:51	A:84982391;C:104532595;G:122785928;T:93918201;N:1070506	51		84982391	104532595	122785928	93918201	1070506	SRX3504481	SRS2782035	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.13902	0.01444	0.99076	0.58988	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Liver	Liver and Biliary System

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