metadata: run_metadata: 83 rows where devstage_curation = "Undetermined" and experiment.library

83 rows where devstage_curation = "Undetermined" and experiment.library_selection = "unspecified"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36405	36405	SRR546820	SRX180750	SRS347212	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.	pubmed:24531765	Zebrafish wild type AB strain embryo prim6 stage	D. rerio prim6 embryo	D. rerio prim6 embryo		RNAseq D. rerio prim6 embryo	RNAseq D. rerio prim6 embryo	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950	RNAseq_prim6_2_fix.fastq	fastq	3011340704.0	19811452.0	RNAseq D. rerio prim6 embryo	0:76 1:76	A:727345664;C:767747833;G:787766862;T:725606403;N:2873942	76	76	727345664	767747833	787766862	725606403	2873942	SRX180750	SRS347212	SRA055273	University of Bergen	ZEPROME consortium	2	0.94491	0.94492	0.04196	0.04323	0.76641	0.76928	0.48087	0.48787	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36581	36581	SRR594769	SRX195432	SRS369361	SRP016134	PRJNA177654	Danio rerio Transcriptome or Gene expression	PRJNA177654	Other	We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.		1	Test	GFP Negative 1		Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development	Embryos	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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>	SRP016134			2525199228.0	65962848.0	GFP Positive	0:38.28	A:665802914;C:594493287;G:612298433;T:652078696;N:525898	38		665802914	594493287	612298433	652078696	525898	SRX195432	SRS369361			University of Cambridge	1	0.89062		0.09595		0.74059		0.47506		36		B		usable mapping rate	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United Kingdom	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36582	36582	SRR594771	SRX195432	SRS369361	SRP016134	PRJNA177654	Danio rerio Transcriptome or Gene expression	PRJNA177654	Other	We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.		1	Test	GFP Negative 1		Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development	Embryos	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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>	SRP016134	gfp_negative_replicate_1_sequence.txt.gz	fastq	2549682148.0	66546682.0	GFP Negative	0:38.31	A:686329592;C:587342682;G:601330559;T:674194074;N:485241	38		686329592	587342682	601330559	674194074	485241	SRX195432	SRS369361			University of Cambridge	1	0.90413		0.13272		0.71342		0.48186		36		B		usable mapping rate	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United Kingdom	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36586	36586	SRR1562528	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			3901027000.0	41246200.0	zebrafish data1	0:50 1:50	A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159	50	50	1065764997	896043530	867105444	1071973870	139159	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95204	0.94561	0.11416	0.11357	0.68235	0.68387	0.47537	0.47688	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36587	36587	SRR1562529	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			3298508150.0	34528793.0	zebrafish data2	0:50 1:50	A:870578872;C:780299206;G:764413584;T:883098619;N:117869	50	50	870578872	780299206	764413584	883098619	117869	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.96195	0.9525	0.05344	0.0528	0.77285	0.7737	0.44453	0.43789	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36588	36588	SRR1562530	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			5033866800.0	52047991.0	zebrafish data6	0:50 1:50	A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438	50	50	1318991279	1193979085	1179037925	1341674073	184438	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.97568	0.97028	0.03448	0.03488	0.88767	0.88785	0.17745	0.18337	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36589	36589	SRR1562531	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			4394828000.0	45714707.0	zebrafish data3	0:50 1:50	A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894	50	50	1146792341	1067826128	1033443384	1146608253	157894	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.96496	0.95999	0.03952	0.03946	0.78571	0.78518	0.51359	0.49202	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36590	36590	SRR1562532	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			3637203400.0	38182310.0	zebrafish data4	0:50 1:50	A:956604323;C:863740756;G:843429871;T:973297634;N:130816	50	50	956604323	863740756	843429871	973297634	130816	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95377	0.94653	0.0656	0.06507	0.72448	0.72541	0.4157	0.41707	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36591	36591	SRR1562533	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.		Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome		Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135			4185424200.0	44832788.0	zebrafish data5	0:50 1:50	A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807	50	50	1143949920	959926497	921201865	1160194111	151807	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95163	0.94301	0.12015	0.11974	0.64396	0.64514	0.49698	0.49883	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36739	36739	SRR867022	SRX286270	SRS420566	SRP022549	PRJNA202401	Danio rerio Transcriptome or Gene expression	PRJNA202401	Other	Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.		Full transcriptome analysis of early dorsoventral DV patterning in zebrafish	General Sample for Danio rerio	ICH	strain:wild type	Full transcriptome analysis of early dorsoventral DV patterning in zebrafish Bcat	Danio rerio boot	1	RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	<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>	SRP022549	s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta	SOLiD_native SOLiD_native	9801985250.0	196039705.0	Zebrafish DV patterning Boot	0:50	0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939	50							SRX286270	SRS420566	SRA075737	BAYGEN\|NGSP	BAYGEN	1	0.59289		0.09435		0.92669		0.7658		50		B		usable mapping rate	legacy	early	3prime	rrna_depletion	unknown	bulk	unknown	unknown	Hungary	2013-05-23	Undetermined	Undetermined	Undetermined	Undetermined
36740	36740	SRR867023	SRX286271	SRS420566	SRP022549	PRJNA202401	Danio rerio Transcriptome or Gene expression	PRJNA202401	Other	Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.		Full transcriptome analysis of early dorsoventral DV patterning in zebrafish	General Sample for Danio rerio	ICH	strain:wild type	Full transcriptome analysis of early dorsoventral DV patterning in zebrafish ICH	Danio rerio ICH	1	RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	<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>	SRP022549	s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual	SOLiD_native SOLiD_native	10810535400.0	216210708.0	Zebrafish DV patterning ICH	0:50	0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417	50							SRX286271	SRS420566	SRA075737	BAYGEN\|NGSP	BAYGEN	1	0.42474		0.06136		0.93434		0.75757		50		B		usable mapping rate	legacy	early	3prime	rrna_depletion	unknown	bulk	unknown	unknown	Hungary	2013-05-23	Undetermined	Undetermined	Undetermined	Undetermined
41381	41381	SRR4375307	SRX2226800	SRS1732678	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B1	resa AG01072	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B1	AG01072.1	AG01072.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz	fastq fastq	756436968.0	4976559.0	AG01072.1 R2.fastq.gz	0:76 1:76	A:277813562;C:101592220;G:103435859;T:273576694;N:18633	76	76	277813562	101592220	103435859	273576694	18633	SRX2226800	SRS1732678	SRA482696	Yale University\|Genetics	Yale University	2	0.00777	0.00795	0.00043	0.00056	0.99344	0.99389	0.43869	0.43095	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-10-06	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41397	41397	SRR4375099	SRX2226671	SRS1732680	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B3	resa AG01074	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B3	AG01074.2	AG01074.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz	fastq fastq	1411678568.0	9287359.0	AG01074.2 R1.fastq.gz	0:76 1:76	A:518452828;C:189515599;G:191777773;T:511511925;N:420443	76	76	518452828	189515599	191777773	511511925	420443	SRX2226671	SRS1732680	SRA482696	Yale University\|Genetics	Yale University	2	0.00745	0.00729	0.00047	0.00045	0.99405	0.99411	0.43814	0.47981	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41398	41398	SRR4375098	SRX2226670	SRS1732680	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B3	resa AG01074	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B3	AG01074.1	AG01074.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01074.1_R1.fastq.gz AG01074.1_R2.fastq.gz	fastq fastq	867077312.0	5704456.0	AG01074.1 R1.fastq.gz	0:76 1:76	A:318238609;C:116633576;G:118737324;T:313446459;N:21344	76	76	318238609	116633576	118737324	313446459	21344	SRX2226670	SRS1732680	SRA482696	Yale University\|Genetics	Yale University	2	0.00791	0.00753	0.00052	0.00054	0.99395	0.99381	0.45038	0.44477	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41399	41399	SRR4375097	SRX2226669	SRS1732679	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B2	resa AG01073	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B2	AG01073.2	AG01073.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01073.2_R1.fastq.gz AG01073.2_R2.fastq.gz	fastq fastq	1170921968.0	7703434.0	AG01073.2 R1.fastq.gz	0:76 1:76	A:430252673;C:156958676;G:158824982;T:424542052;N:343585	76	76	430252673	156958676	158824982	424542052	343585	SRX2226669	SRS1732679	SRA482696	Yale University\|Genetics	Yale University	2	0.00759	0.00753	0.00044	0.00046	0.99389	0.99375	0.48023	0.49305	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41400	41400	SRR4375096	SRX2226668	SRS1732679	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B2	resa AG01073	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B2	AG01073.1	AG01073.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01073.1_R1.fastq.gz AG01073.1_R2.fastq.gz	fastq fastq	650729936.0	4281118.0	AG01073.1 R1.fastq.gz	0:76 1:76	A:238957997;C:87418913;G:88996057;T:235340339;N:16630	76	76	238957997	87418913	88996057	235340339	16630	SRX2226668	SRS1732679	SRA482696	Yale University\|Genetics	Yale University	2	0.00771	0.00754	0.00052	0.00049	0.99403	0.9936	0.46484	0.42136	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41401	41401	SRR4375095	SRX2226667	SRS1732678	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B1	resa AG01072	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B1	AG01072.2	AG01072.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01072.2_R1.fastq.gz AG01072.2_R2.fastq.gz	fastq fastq	1293717904.0	8511302.0	AG01072.2 R1.fastq.gz	0:76 1:76	A:475476006;C:173352933;G:175448573;T:469059516;N:380876	76	76	475476006	173352933	175448573	469059516	380876	SRX2226667	SRS1732678	SRA482696	Yale University\|Genetics	Yale University	2	0.0072	0.0071	0.00042	0.00038	0.99397	0.99385	0.4403	0.43351	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41403	41403	SRR4375093	SRX2226665	SRS1732676	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Needle r2	resa AG00580	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|condition:needle\|BioSampleModel:Model organism or animal	RESA Seq Needle r2	AG00580.1	AG00580.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG00580.1_R1.fastq.gz AG00580.1_R2.fastq.gz	fastq fastq	536691936.0	3530868.0	AG00580.1 R1.fastq.gz	0:76 1:76	A:162711942;C:106417027;G:106484569;T:160130705;N:947693	76	76	162711942	106417027	106484569	160130705	947693	SRX2226665	SRS1732676	SRA482696	Yale University\|Genetics	Yale University	2	0.85835	0.85877	0.03686	0.03615	0.96818	0.96895	0.47111	0.47948	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41827	41827	SRR5251446	SRX2557171	SRS1974564	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B1	nicoli mutmir AG01645	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B1	AG01645.1	AG01645.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01645.1_R1.fastq.gz	fastq	1574284140.0	20714265.0	AG01645.1 R1.fastq.gz	0:76	A:485471345;C:270854124;G:374164721;T:443766613;N:27337	76		485471345	270854124	374164721	443766613	27337	SRX2557171	SRS1974564	SRA537606	Yale University\|Genetics	Yale University	1	0.82142		0.14068		0.8002		0.5444		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-27	Undetermined	Embryo	Endothelium	Cardiovascular System
41828	41828	SRR5251445	SRX2557170	SRS1974563	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B2	nicoli mutmir AG01646	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B2	AG01646.1	AG01646.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01646.1_R1.fastq.gz	fastq	1484740104.0	19536054.0	AG01646.1 R1.fastq.gz	0:76	A:453388316;C:246477203;G:365031959;T:419816346;N:26280	76		453388316	246477203	365031959	419816346	26280	SRX2557170	SRS1974563	SRA537606	Yale University\|Genetics	Yale University	1	0.82649		0.1897		0.79862		0.52759		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41829	41829	SRR5251444	SRX2557169	SRS1974562	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B3	nicoli mutmir AG01647	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B3	AG01647.1	AG01647.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01647.1_R1.fastq.gz	fastq	881298660.0	11596035.0	AG01647.1 R1.fastq.gz	0:76	A:270675838;C:160127586;G:228157662;T:222301246;N:36328	76		270675838	160127586	228157662	222301246	36328	SRX2557169	SRS1974562	SRA537606	Yale University\|Genetics	Yale University	1	0.76133		0.15034		0.83341		0.56596		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41830	41830	SRR5251443	SRX2557168	SRS1974561	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B1	nicoli mutmir AG01648	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B1	AG01648.1	AG01648.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01648.1_R1.fastq.gz	fastq	637896880.0	8393380.0	AG01648.1 R1.fastq.gz	0:76	A:192829278;C:112701153;G:153321271;T:179019095;N:26083	76		192829278	112701153	153321271	179019095	26083	SRX2557168	SRS1974561	SRA537606	Yale University\|Genetics	Yale University	1	0.75971		0.1181		0.82171		0.56797		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41831	41831	SRR5251442	SRX2557167	SRS1974560	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B2	nicoli mutmir AG01649	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B2	AG01649.1	AG01649.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01649.1_R1.fastq.gz	fastq	849868328.0	11182478.0	AG01649.1 R1.fastq.gz	0:76	A:258225905;C:148467172;G:205165181;T:237974100;N:35970	76		258225905	148467172	205165181	237974100	35970	SRX2557167	SRS1974560	SRA537606	Yale University\|Genetics	Yale University	1	0.75096		0.14506		0.81507		0.5545		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41832	41832	SRR5251441	SRX2557166	SRS1974559	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B3	nicoli mutmir AG01650	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B3	AG01650.1	AG01650.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01650.1_R1.fastq.gz	fastq	998464668.0	13137693.0	AG01650.1 R1.fastq.gz	0:76	A:311526420;C:176545041;G:251852786;T:258497630;N:42791	76		311526420	176545041	251852786	258497630	42791	SRX2557166	SRS1974559	SRA537606	Yale University\|Genetics	Yale University	1	0.76479		0.11192		0.82674		0.54621		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41833	41833	SRR5251440	SRX2557165	SRS1974558	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B1	nicoli mutmir AG01651	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B1	AG01651.1	AG01651.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01651.1_R1.fastq.gz	fastq	570492252.0	7506477.0	AG01651.1 R1.fastq.gz	0:76	A:162512811;C:104071716;G:135730697;T:168149427;N:27601	76		162512811	104071716	135730697	168149427	27601	SRX2557165	SRS1974558	SRA537606	Yale University\|Genetics	Yale University	1	0.73988		0.10157		0.86647		0.54252		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41834	41834	SRR5251439	SRX2557164	SRS1974557	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B2	nicoli mutmir AG01652	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B2	AG01652.1	AG01652.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01652.1_R1.fastq.gz	fastq	1072886148.0	14116923.0	AG01652.1 R1.fastq.gz	0:76	A:338399596;C:192703439;G:242960887;T:298769761;N:52465	76		338399596	192703439	242960887	298769761	52465	SRX2557164	SRS1974557	SRA537606	Yale University\|Genetics	Yale University	1	0.76456		0.11024		0.89197		0.59214		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41835	41835	SRR5251438	SRX2557163	SRS1974556	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B3	nicoli mutmir AG01653	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B3	AG01653.1	AG01653.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01653.1_R1.fastq.gz	fastq	1016374144.0	13373344.0	AG01653.1 R1.fastq.gz	0:76	A:310958343;C:168702106;G:223420046;T:313241363;N:52286	76		310958343	168702106	223420046	313241363	52286	SRX2557163	SRS1974556	SRA537606	Yale University\|Genetics	Yale University	1	0.75735		0.12224		0.79756		0.55136		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41836	41836	SRR5251437	SRX2557162	SRS1974555	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B1	nicoli mutmir AG01654	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B1	AG01654.1	AG01654.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01654.1_R1.fastq.gz	fastq	782170112.0	10291712.0	AG01654.1 R1.fastq.gz	0:76	A:238316720;C:132163709;G:179301544;T:232350598;N:37541	76		238316720	132163709	179301544	232350598	37541	SRX2557162	SRS1974555	SRA537606	Yale University\|Genetics	Yale University	1	0.7683		0.10712		0.80034		0.55804		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41837	41837	SRR5251436	SRX2557161	SRS1974554	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B2	nicoli mutmir AG01655	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B2	AG01655.1	AG01655.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01655.1_R1.fastq.gz	fastq	1053946340.0	13867715.0	AG01655.1 R1.fastq.gz	0:76	A:318351311;C:191163031;G:240348413;T:304030367;N:53218	76		318351311	191163031	240348413	304030367	53218	SRX2557161	SRS1974554	SRA537606	Yale University\|Genetics	Yale University	1	0.77588		0.07983		0.83934		0.56228		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41838	41838	SRR5251435	SRX2557160	SRS1974553	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B3	nicoli mutmir AG01656	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B3	AG01656.1	AG01656.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01656.1_R1.fastq.gz	fastq	1182467736.0	15558786.0	AG01656.1 R1.fastq.gz	0:76	A:344465226;C:204677242;G:269228338;T:364036735;N:60195	76		344465226	204677242	269228338	364036735	60195	SRX2557160	SRS1974553	SRA537606	Yale University\|Genetics	Yale University	1	0.78956		0.13495		0.81517		0.56342		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41839	41839	SRR5251434	SRX2557159	SRS1974552	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B1	nicoli mutmir AG01657	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B1	AG01657.1	AG01657.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01657.1_R1.fastq.gz	fastq	536336712.0	7057062.0	AG01657.1 R1.fastq.gz	0:76	A:158301607;C:93070120;G:121382262;T:163555487;N:27236	76		158301607	93070120	121382262	163555487	27236	SRX2557159	SRS1974552	SRA537606	Yale University\|Genetics	Yale University	1	0.76425		0.1278		0.84222		0.55305		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41840	41840	SRR5251433	SRX2557158	SRS1974551	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B2	nicoli mutmir AG01658	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B2	AG01658.1	AG01658.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01658.1_R1.fastq.gz	fastq	798581856.0	10507656.0	AG01658.1 R1.fastq.gz	0:76	A:241352089;C:134327379;G:183394123;T:239469845;N:38420	76		241352089	134327379	183394123	239469845	38420	SRX2557158	SRS1974551	SRA537606	Yale University\|Genetics	Yale University	1	0.76221		0.13398		0.82459		0.55228		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41841	41841	SRR5251432	SRX2557157	SRS1974550	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B3	nicoli mutmir AG01659	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B3	AG01659.1	AG01659.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01659.1_R1.fastq.gz	fastq	1093998948.0	14394723.0	AG01659.1 R1.fastq.gz	0:76	A:330741822;C:186325335;G:249557623;T:327320449;N:53719	76		330741822	186325335	249557623	327320449	53719	SRX2557157	SRS1974550	SRA537606	Yale University\|Genetics	Yale University	1	0.77108		0.14674		0.80955		0.55819		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41842	41842	SRR5251431	SRX2557156	SRS1974549	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR223 B1	nicoli mutmir AG01660	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR223 B1	AG01660.1	AG01660.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01660.1_R1.fastq.gz	fastq	849905492.0	11182967.0	AG01660.1 R1.fastq.gz	0:76	A:250953875;C:146191904;G:190040699;T:262674911;N:44103	76		250953875	146191904	190040699	262674911	44103	SRX2557156	SRS1974549	SRA537606	Yale University\|Genetics	Yale University	1	0.7687		0.14192		0.82842		0.5344		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41843	41843	SRR5251430	SRX2557155	SRS1974548	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR223 B2	nicoli mutmir AG01661	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR223 B2	AG01661.1	AG01661.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466	AG01661.1_R1.fastq.gz	fastq	840115400.0	11054150.0	AG01661.1 R1.fastq.gz	0:76	A:257057495;C:141775085;G:188281166;T:252960590;N:41064	76		257057495	141775085	188281166	252960590	41064	SRX2557155	SRS1974548	SRA537606	Yale University\|Genetics	Yale University	1	0.74292		0.10759		0.83615		0.55136		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
42492	42492	SRR5681431	SRX2916758	SRS2282896	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				15um	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:15um\|BioSampleModel:Model organism or animal	15um zebrafish	15um zebrafish	15um zebrafish	15um zebrafish	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143	15um_2.fq.gz 15um_1.fq.gz	fastq fastq	4510379400.0	22551897.0	15um 2.fq.gz	0:100 1:100	A:1183709237;C:1078933188;G:1057042534;T:1190615427;N:79014	100	100	1183709237	1078933188	1057042534	1190615427	79014	SRX2916758	SRS2282896	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.95073	0.95055	0.0647	0.06526	0.67176	0.67351	0.46247	0.46176	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
42493	42493	SRR5681432	SRX2916757	SRS2282895	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				10um	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:10um\|BioSampleModel:Model organism or animal	10um zebrafish	10um zebrafish	10um zebrafish	10um zebrafish	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143	10um_1.fq.gz 10um_2.fq.gz	fastq fastq	4513300800.0	22566504.0	10um 1.fq.gz	0:100 1:100	A:1186008993;C:1078123999;G:1056044415;T:1193043558;N:79835	100	100	1186008993	1078123999	1056044415	1193043558	79835	SRX2916757	SRS2282895	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.94799	0.94687	0.07002	0.06979	0.66667	0.66746	0.47255	0.47338	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
42494	42494	SRR5681433	SRX2916756	SRS2282894	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				control	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:control\|BioSampleModel:Model organism or animal	control zebrafish	control zebrafish	control zebrafish	control zebrafish	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143	con_1.fq.gz con_2.fq.gz	fastq fastq	4514603400.0	22573017.0	con 2.fq.gz	0:100 1:100	A:1183878943;C:1081336890;G:1058805201;T:1190503424;N:78942	100	100	1183878943	1081336890	1058805201	1190503424	78942	SRX2916756	SRS2282894	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.951	0.95009	0.0669	0.06735	0.6659	0.66681	0.46599	0.46703	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43083	43083	SRR7264587	SRX4168710	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270	strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.4;AG01270.4	AG01269.4;AG01270.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	C7MYYANXX_JBCX101_016_R1.fastq.gz	fastq	3504515800.0	46112050.0	C7MYYANXX JBCX101 016 R1.fastq.gz	0:76	A:1100987855;C:897481291;G:850509260;T:655386223;N:151171	76		1100987855	897481291	850509260	655386223	151171	SRX4168710	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00251		0.00024		0.99334		0.49363		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43084	43084	SRR7264588	SRX4168709	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270	strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.3;AG01270.3	AG01269.3;AG01270.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	HVJ7NADXX_JBCX101_016_R1.fastq.gz	fastq	1533760484.0	20181059.0	HVJ7NADXX JBCX101 016 R1.fastq.gz	0:76	A:486730101;C:387546602;G:372319444;T:287072948;N:91389	76		486730101	387546602	372319444	287072948	91389	SRX4168709	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	4e-05		2e-05		0.99997		1.0		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43086	43086	SRR7264590	SRX4168707	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270	strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.5;AG01270.5	AG01269.5;AG01270.5	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	C7MWLANXX_JBCX101_016_R1.fastq.gz	fastq	11187105076.0	147198751.0	C7MWLANXX JBCX101 016 R1.fastq.gz	0:76	A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660	76		3525623658	2869684594	2708534500	2083102664	159660	SRX4168707	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43089	43089	SRR7264593	SRX4168704	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270	strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.2;AG01270.2	AG01269.2;AG01270.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	HVK53ADXX_JBCX101_016_R1.fastq.gz	fastq	4318423208.0	56821358.0	HVK53ADXX JBCX101 016 R1.fastq.gz	0:76	A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019	76		1370691469	1101595011	1048719303	796936406	481019	SRX4168704	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	1e-05		0.0		0.99997		0.0		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43090	43090	SRR7264594	SRX4168703	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270	strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.1;AG01270.1	AG01269.1;AG01270.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	HMHGVADXX_JBCX101_016_R1.fastq.gz	fastq	3247405520.0	42729020.0	HMHGVADXX JBCX101 016 R1.fastq.gz	0:76	A:1030573532;C:829398246;G:789085434;T:598013908;N:334400	76		1030573532	829398246	789085434	598013908	334400	SRX4168703	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43095	43095	SRR5893054	SRX3058791	SRS2404524	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			miniRESA 2h pA RNA B1	miniresa AG01710	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:25\|replicate:1\|BioSampleModel:Model organism or animal	miniRESA 2h pA RNA B1	AG01710.1	AG01710.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01710.1_R1.fastq.gz	fastq	236178588.0	3107613.0	AG01710.1 R1.fastq.gz	0:76	A:63902747;C:43772893;G:46507615;T:81990822;N:4511	76		63902747	43772893	46507615	81990822	4511	SRX3058791	SRS2404524	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.92111		4e-05		0.99799		0.56316		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43096	43096	SRR5893055	SRX3058790	SRS2404526	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			miniRESA 2h pA RNA B2	miniresa AG01711	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:25\|replicate:2\|BioSampleModel:Model organism or animal	miniRESA 2h pA RNA B2	AG01711.1	AG01711.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01711.1_R1.fastq.gz	fastq	226089360.0	2974860.0	AG01711.1 R1.fastq.gz	0:76	A:61341697;C:41846683;G:44622362;T:78273216;N:5402	76		61341697	41846683	44622362	78273216	5402	SRX3058790	SRS2404526	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.91845		1e-05		0.99797		0.60522		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43153	43153	SRR5893120	SRX3058725	SRS2404546	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B2	dmsseq AG01269	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B2	AG01269.2	AG01269.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01269.2_R1.fastq.gz	fastq	615648941.0	27257391.0	AG01269.2 R1.fastq.gz	0:22.59 1:0	A:163885634;C:143593857;G:157437520;T:150675530;N:56400	22	0	163885634	143593857	157437520	150675530	56400	SRX3058725	SRS2404546	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.6277		0.07639		0.78236		0.60487		20		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43154	43154	SRR5893121	SRX3058724	SRS2404546	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B2	dmsseq AG01269	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B2	AG01269.1	AG01269.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01269.1_R1.fastq.gz	fastq	461341500.0	20486790.0	AG01269.1 R1.fastq.gz	0:22.52 1:0	A:122338299;C:107915972;G:118163678;T:112917569;N:5982	22	0	122338299	107915972	118163678	112917569	5982	SRX3058724	SRS2404546	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.62415		0.07628		0.78133		0.60032		19		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43159	43159	SRR8782100	SRX3058719	SRS2404551	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			miniRESA 2h pA RNA B4	miniresa AG01728	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:25\|replicate:4\|BioSampleModel:Model organism or animal	miniRESA 2h pA RNA B4	AG01728.1	AG01728.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	SRR5893126_replace_R1.fastq.gz	fastq	156537732.0	2059707.0	SRR5893126 replace R1.fastq.gz	0:76	A:42070748;C:29088642;G:31333987;T:54029008;N:15347	76		42070748	29088642	31333987	54029008	15347	SRX3058719	SRS2404551	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.94152		0.0		0.99797		0.61884		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2019-03-25	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43160	43160	SRR8782101	SRX3058718	SRS2404553	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			miniRESA 2h pA RNA B3	miniresa AG01727	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:25\|replicate:3\|BioSampleModel:Model organism or animal	miniRESA 2h pA RNA B3	AG01727.1	AG01727.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	SRR5893127_replace_R1.fastq.gz	fastq	150519748.0	1980523.0	SRR5893127 replace R1.fastq.gz	0:76	A:40089061;C:28406150;G:30480481;T:51528116;N:15940	76		40089061	28406150	30480481	51528116	15940	SRX3058718	SRS2404553	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.94224		1e-05		0.99793		0.60622		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2019-03-25	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43162	43162	SRR8782104	SRX3058716	SRS2404554	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			miniRESA 2h pA RNA B5	miniresa AG01729	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:25\|replicate:5\|BioSampleModel:Model organism or animal	miniRESA 2h pA RNA B5	AG01729.1	AG01729.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	SRR5893129_replace_R1.fastq.gz	fastq	164152628.0	2159903.0	SRR5893129 replace R1.fastq.gz	0:76	A:44289887;C:30688789;G:32985693;T:56172026;N:16233	76		44289887	30688789	32985693	56172026	16233	SRX3058716	SRS2404554	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.9284		1e-05		0.9976		0.61504		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2019-03-25	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43164	43164	SRR5893131	SRX3058714	SRS2404556	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B1	dmsseq AG01270	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:1\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B1	AG01270.4	AG01270.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01270.4_R1.fastq.gz	fastq	369232203.0	16423574.0	AG01270.4 R1.fastq.gz	0:22.48 1:0	A:96909706;C:86935520;G:96347195;T:89039251;N:531	22	0	96909706	86935520	96347195	89039251	531	SRX3058714	SRS2404556	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.61992		0.07599		0.78701		0.61408		22		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43165	43165	SRR5893132	SRX3058713	SRS2404556	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B1	dmsseq AG01270	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:1\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B1	AG01270.5	AG01270.5	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01270.5_R1.fastq.gz	fastq	1209837988.0	53770802.0	AG01270.5 R1.fastq.gz	0:22.50 1:0	A:315203598;C:286991445;G:317405494;T:290233476;N:3975	22	0	315203598	286991445	317405494	290233476	3975	SRX3058713	SRS2404556	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.628		0.07601		0.78675		0.61598		27		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43166	43166	SRR5893133	SRX3058712	SRS2404556	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B1	dmsseq AG01270	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:1\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B1	AG01270.2	AG01270.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01270.2_R1.fastq.gz	fastq	475556869.0	21124005.0	AG01270.2 R1.fastq.gz	0:22.51 1:0	A:125248500;C:112069047;G:123791782;T:114403721;N:43819	22	0	125248500	112069047	123791782	114403721	43819	SRX3058712	SRS2404556	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.62492		0.07783		0.78451		0.5998		22		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43167	43167	SRR5893134	SRX3058711	SRS2404556	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B1	dmsseq AG01270	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:1\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B1	AG01270.3	AG01270.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01270.3_R1.fastq.gz	fastq	161875687.0	7179709.0	AG01270.3 R1.fastq.gz	0:22.55 1:0	A:42971355;C:37785152;G:42094982;T:39023778;N:420	22	0	42971355	37785152	42094982	39023778	420	SRX3058711	SRS2404556	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.62849		0.07622		0.78307		0.60361		27		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43168	43168	SRR5893135	SRX3058710	SRS2404546	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B2	dmsseq AG01269	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B2	AG01269.5	AG01269.5	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01269.5_R1.fastq.gz	fastq	1563607961.0	69286414.0	AG01269.5 R1.fastq.gz	0:22.57 1:0	A:411693836;C:367369547;G:402702896;T:381836642;N:5040	22	0	411693836	367369547	402702896	381836642	5040	SRX3058710	SRS2404546	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.62646		0.07519		0.78332		0.60197		26		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43169	43169	SRR5893136	SRX3058709	SRS2404556	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B1	dmsseq AG01270	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:1\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B1	AG01270.1	AG01270.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01270.1_R1.fastq.gz	fastq	355558938.0	15838601.0	AG01270.1 R1.fastq.gz	0:22.45 1:0	A:93238299;C:84024450;G:92763663;T:85527926;N:4600	22	0	93238299	84024450	92763663	85527926	4600	SRX3058709	SRS2404556	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.62041		0.07796		0.78526		0.60168		15		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43170	43170	SRR5893137	SRX3058708	SRS2404546	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B2	dmsseq AG01269	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B2	AG01269.3	AG01269.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01269.3_R1.fastq.gz	fastq	212697329.0	9397171.0	AG01269.3 R1.fastq.gz	0:22.63 1:0	A:57025177;C:49118963;G:54415396;T:52137277;N:516	22	0	57025177	49118963	54415396	52137277	516	SRX3058708	SRS2404546	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.63192		0.07668		0.77983		0.6006		20		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43171	43171	SRR5893138	SRX3058707	SRS2404546	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			DMS Seq IVT 64c B2	dmsseq AG01269	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2\|BioSampleModel:Model organism or animal	DMS Seq IVT 64c B2	AG01269.4	AG01269.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01269.4_R1.fastq.gz	fastq	474396378.0	21071500.0	AG01269.4 R1.fastq.gz	0:22.51 1:0	A:125988009;C:110649678;G:121336327;T:116421641;N:723	22	0	125988009	110649678	121336327	116421641	723	SRX3058707	SRS2404546	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.6211		0.07454		0.78612		0.60194		21		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
46213	46213	SRR6477201	SRX3567063	SRS2838995	SRP129892	PRJNA430431	RES complex is associated with intron definition and required for zebrafish early embryogenesis	PRJNA430431	Other	Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.			RNAseq RES complex rbmx2 SIB 48h	RNAseq RES complex rbmx2 SIB 48h AG01558	strain:TU/AB\|age:48.0\|sex:pooled male and female\|tissue:embryo\|genotype:+/?\|molecule:mRNA\|selection:pA\|replicate group:4\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq RES complex rbmx2 SIB 48h	AG01558.1	AG01558.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP129892	AG01558.1_R1.fastq.gz AG01558.1_R2.fastq.gz	fastq fastq	9241524912.0	60799506.0	AG01558.1 R2.fastq.gz	0:76 1:76	A:2590261461;C:2051008707;G:2048932825;T:2547072369;N:4249550	76	76	2590261461	2051008707	2048932825	2547072369	4249550	SRX3567063	SRS2838995	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.94691	0.94614	0.14206	0.14368	0.68093	0.68004	0.46358	0.46633	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-23	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
46214	46214	SRR6477202	SRX3567062	SRS2838994	SRP129892	PRJNA430431	RES complex is associated with intron definition and required for zebrafish early embryogenesis	PRJNA430431	Other	Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.			RNAseq RES complex rbmx2 KO 48h	RNAseq RES complex rbmx2 KO 48h AG01557	strain:TU/AB\|age:48.0\|sex:pooled male and female\|tissue:embryo\|genotype: / \|molecule:mRNA\|selection:pA\|replicate group:3\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq RES complex rbmx2 KO 48h	AG01557.1	AG01557.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP129892	AG01557.1_R1.fastq.gz AG01557.1_R2.fastq.gz	fastq fastq	10308923480.0	67821865.0	AG01557.1 R2.fastq.gz	0:76 1:76	A:2867250947;C:2265018715;G:2268705348;T:2903182748;N:4765722	76	76	2867250947	2265018715	2268705348	2903182748	4765722	SRX3567062	SRS2838994	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93752	0.94003	0.18012	0.18634	0.68893	0.6858	0.46131	0.46347	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-23	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
46215	46215	SRR6477203	SRX3567061	SRS2838993	SRP129892	PRJNA430431	RES complex is associated with intron definition and required for zebrafish early embryogenesis	PRJNA430431	Other	Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.			RNAseq RES complex snip1 SIB 48h	RNAseq RES complex snip1 SIB 48h AG01560	strain:TU/AB\|age:48.0\|sex:pooled male and female\|tissue:embryo\|genotype:+/?\|molecule:mRNA\|selection:pA\|replicate group:6\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq RES complex snip1 SIB 48h	AG01560.1	AG01560.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP129892	AG01560.1_R1.fastq.gz AG01560.1_R2.fastq.gz	fastq fastq	12336748336.0	81162818.0	AG01560.1 R2.fastq.gz	0:76 1:76	A:3381905039;C:2782580059;G:2774648248;T:3391983732;N:5631258	76	76	3381905039	2782580059	2774648248	3391983732	5631258	SRX3567061	SRS2838993	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.94802	0.9492	0.13035	0.13145	0.68006	0.67783	0.46768	0.46426	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-23	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
46216	46216	SRR6477204	SRX3567060	SRS2838992	SRP129892	PRJNA430431	RES complex is associated with intron definition and required for zebrafish early embryogenesis	PRJNA430431	Other	Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.			RNAseq RES complex snip1 KO 48h	RNAseq RES complex snip1 KO 48h AG01559	strain:TU/AB\|age:48.0\|sex:pooled male and female\|tissue:embryo\|genotype: / \|molecule:mRNA\|selection:pA\|replicate group:5\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq RES complex snip1 KO 48h	AG01559.1	AG01559.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP129892	AG01559.1_R1.fastq.gz AG01559.1_R2.fastq.gz	fastq fastq	11252234568.0	74027859.0	AG01559.1 R1.fastq.gz	0:76 1:76	A:3167425566;C:2465030272;G:2448402147;T:3166105639;N:5270944	76	76	3167425566	2465030272	2448402147	3166105639	5270944	SRX3567060	SRS2838992	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93557	0.9354	0.19378	0.19524	0.69075	0.6943	0.46751	0.47134	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-23	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51153	51153	SRR8552545	SRX5354345	SRS4345563	SRP184786	PRJNA521558	Brd4 and p300 confer transcriptional competency during zygotic genome activation	PRJNA521558	Other	The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.			mRNA seq 4h trip R0	mRNA seq 4h trip R0 AGN001745	strain:TU/AB\|age:4.0\|sex:pooled male and female\|tissue:embryo\|treatment:triptolide\|molecule:RNA\|selection:r0\|sample ref:AGS001391\|replicate ref:AGN001745\|replicate order:1\|BioSampleModel:Model organism or animal	mRNA seq 4h trip R0	AGR002401	AGR002401	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP184786	AGR002401_R1.fastq.gz	fastq	924494628.0	12164403.0	AGR002401 R1.fastq.gz	0:76	A:189288361;C:252171181;G:262503967;T:220509369;N:21750	76		189288361	252171181	262503967	220509369	21750	SRX5354345	SRS4345563	SRA847217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.69029		0.07606		0.77516		0.52854		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-06-12	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51334	51334	SRR8784145	SRX5574146	SRS4536707	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h a Am r2 B1	RESA WT 6h a Am r2 B1 AGN000583	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|sample ref:AGS000533\|replicate ref:AGN000583\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT 6h a Am r2 B1	AGR000772	AGR000772	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000772_R1.fastq.gz AGR000772_R2.fastq.gz	fastq fastq	858051704.0	5645077.0	AGR000772 R1.fastq.gz	0:76 1:76	A:260528161;C:169740216;G:169821501;T:256446553;N:1515273	76	76	260528161	169740216	169821501	256446553	1515273	SRX5574146	SRS4536707	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85086	0.85133	0.03656	0.0362	0.96861	0.96917	0.47155	0.47528	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51336	51336	SRR8784147	SRX5574144	SRS4536704	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT TinyLNA430 6h DL B2	RESA WT TinyLNA430 6h DL B2 AGN000468	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000445\|replicate ref:AGN000468\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT TinyLNA430 6h DL B2	AGR000602	AGR000602	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000602_R1.fastq.gz	fastq	2627525732.0	34572707.0	AGR000602 R1.fastq.gz	0:76	A:750015324;C:666424084;G:623763820;T:586999539;N:322965	76		750015324	666424084	623763820	586999539	322965	SRX5574144	SRS4536704	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87853		0.06924		0.78255		0.55641		76		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51337	51337	SRR8784148	SRX5574143	SRS4536697	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT TinyLNA430 6h DL B1	RESA WT TinyLNA430 6h DL B1 AGN000467	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000445\|replicate ref:AGN000467\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT TinyLNA430 6h DL B1	AGR000601	AGR000601	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000601_R1.fastq.gz	fastq	3663991464.0	48210414.0	AGR000601 R1.fastq.gz	0:76	A:1047383844;C:920761577;G:959252939;T:736380253;N:212851	76		1047383844	920761577	959252939	736380253	212851	SRX5574143	SRS4536697	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00056		0.00017		0.99868		0.34782		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51339	51339	SRR8784150	SRX5574141	SRS4536704	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT TinyLNA430 6h DL B2	RESA WT TinyLNA430 6h DL B2 AGN000468	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000445\|replicate ref:AGN000468\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT TinyLNA430 6h DL B2	AGR000603	AGR000603	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000603_R1.fastq.gz	fastq	3393300668.0	44648693.0	AGR000603 R1.fastq.gz	0:76	A:969581621;C:868752008;G:809775803;T:744990313;N:200923	76		969581621	868752008	809775803	744990313	200923	SRX5574141	SRS4536704	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87891		0.06856		0.78317		0.55832		76		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51340	51340	SRR8784151	SRX5574140	SRS4536703	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h a Am r2 B2	RESA WT 6h a Am r2 B2 AGN000588	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|sample ref:AGS000533\|replicate ref:AGN000588\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h a Am r2 B2	AGR000774	AGR000774	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000774_R1.fastq.gz AGR000774_R2.fastq.gz	fastq fastq	1137810440.0	7485595.0	AGR000774 R1.fastq.gz	0:76 1:76	A:346292154;C:224190817;G:225113116;T:340741657;N:1472696	76	76	346292154	224190817	225113116	340741657	1472696	SRX5574140	SRS4536703	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85647	0.85773	0.03665	0.03596	0.96964	0.97035	0.4856	0.4814	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51341	51341	SRR8784152	SRX5574139	SRS4536703	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h a Am r2 B2	RESA WT 6h a Am r2 B2 AGN000588	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|sample ref:AGS000533\|replicate ref:AGN000588\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h a Am r2 B2	AGR000773	AGR000773	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000773_R1.fastq.gz AGR000773_R2.fastq.gz	fastq fastq	339886896.0	2236098.0	AGR000773 R1.fastq.gz	0:76 1:76	A:103041077;C:67427767;G:67512829;T:101310772;N:594451	76	76	103041077	67427767	67512829	101310772	594451	SRX5574139	SRS4536703	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.8468	0.84687	0.03641	0.03637	0.96921	0.96901	0.47811	0.47989	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51354	51354	SRR8784165	SRX5574126	SRS4536688	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B2	RESA WT a Am 6h DL B2 AGN000466	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000466\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B2	AGR000599	AGR000599	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000599_R1.fastq.gz	fastq	598577064.0	7876014.0	AGR000599 R1.fastq.gz	0:76	A:173027792;C:152514326;G:149669126;T:123341073;N:24747	76		173027792	152514326	149669126	123341073	24747	SRX5574126	SRS4536688	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00013		1e-05		0.99963		0.52631		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51355	51355	SRR8784166	SRX5574125	SRS4536697	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT TinyLNA430 6h DL B1	RESA WT TinyLNA430 6h DL B1 AGN000467	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000445\|replicate ref:AGN000467\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT TinyLNA430 6h DL B1	AGR000600	AGR000600	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000600_R1.fastq.gz	fastq	2926686508.0	38509033.0	AGR000600 R1.fastq.gz	0:76	A:834684269;C:728545827;G:762223876;T:600884916;N:347620	76		834684269	728545827	762223876	600884916	347620	SRX5574125	SRS4536697	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00012		1e-05		0.99969		0.6		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51356	51356	SRR8784167	SRX5574124	SRS4536696	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h L430 r2 B3	RESA WT 6h L430 r2 B3 AGN000593	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000534\|replicate ref:AGN000593\|replicate order:3\|BioSampleModel:Model organism or animal	RESA WT 6h L430 r2 B3	AGR000779	AGR000779	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000779_R1.fastq.gz AGR000779_R2.fastq.gz	fastq fastq	889245296.0	5850298.0	AGR000779 R1.fastq.gz	0:76 1:76	A:272234472;C:173681747;G:173883274;T:267900144;N:1545659	76	76	272234472	173681747	173883274	267900144	1545659	SRX5574124	SRS4536696	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84547	0.84612	0.03639	0.03635	0.96944	0.97039	0.48497	0.48773	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51358	51358	SRR8784169	SRX5574122	SRS4536694	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h L430 r2 B2	RESA WT 6h L430 r2 B2 AGN000589	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000534\|replicate ref:AGN000589\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h L430 r2 B2	AGR000777	AGR000777	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000777_R2.fastq.gz AGR000777_R1.fastq.gz	fastq fastq	196328368.0	1291634.0	AGR000777 R1.fastq.gz	0:76 1:76	A:59795542;C:38713329;G:38666257;T:58817928;N:335312	76	76	59795542	38713329	38666257	58817928	335312	SRX5574122	SRS4536694	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84756	0.84807	0.03654	0.03624	0.9694	0.96934	0.46519	0.47071	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-03-25	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51359	51359	SRR8784170	SRX5574121	SRS4536694	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h L430 r2 B2	RESA WT 6h L430 r2 B2 AGN000589	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000534\|replicate ref:AGN000589\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h L430 r2 B2	AGR000778	AGR000778	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000778_R1.fastq.gz AGR000778_R2.fastq.gz	fastq fastq	533214328.0	3507989.0	AGR000778 R1.fastq.gz	0:76 1:76	A:162908369;C:104425656;G:104787994;T:160373088;N:719221	76	76	162908369	104425656	104787994	160373088	719221	SRX5574121	SRS4536694	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85621	0.85778	0.03697	0.03641	0.96988	0.96968	0.46864	0.47413	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51360	51360	SRR8784171	SRX5574120	SRS4536693	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h a Am r2 B3	RESA WT 6h a Am r2 B3 AGN000592	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|sample ref:AGS000533\|replicate ref:AGN000592\|replicate order:3\|BioSampleModel:Model organism or animal	RESA WT 6h a Am r2 B3	AGR000775	AGR000775	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000775_R1.fastq.gz AGR000775_R2.fastq.gz	fastq fastq	1104549952.0	7266776.0	AGR000775 R1.fastq.gz	0:76 1:76	A:335891429;C:218153618;G:218325553;T:330250768;N:1928584	76	76	335891429	218153618	218325553	330250768	1928584	SRX5574120	SRS4536693	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84907	0.85057	0.03617	0.03574	0.96944	0.96944	0.48591	0.48735	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51361	51361	SRR8784172	SRX5574119	SRS4536692	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT 6h L430 r2 B1	RESA WT 6h L430 r2 B1 AGN000584	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|sample ref:AGS000534\|replicate ref:AGN000584\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT 6h L430 r2 B1	AGR000776	AGR000776	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000776_R1.fastq.gz AGR000776_R2.fastq.gz	fastq fastq	631123912.0	4152131.0	AGR000776 R1.fastq.gz	0:76 1:76	A:192110171;C:124358889;G:124501405;T:189051826;N:1101621	76	76	192110171	124358889	124501405	189051826	1101621	SRX5574119	SRS4536692	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84407	0.84597	0.03569	0.0355	0.96972	0.96988	0.47078	0.47862	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51363	51363	SRR8784174	SRX5574117	SRS4536690	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B1	RESA WT a Am 6h DL B1 AGN000465	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000465\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B1	AGR000593	AGR000593	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000593_R1.fastq.gz	fastq	169214000.0	2226500.0	AGR000593 R1.fastq.gz	0:76	A:48502801;C:44879333;G:42196735;T:33629068;N:6063	76		48502801	44879333	42196735	33629068	6063	SRX5574117	SRS4536690	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.75523		0.05708		0.79868		0.56487		76		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51364	51364	SRR8784175	SRX5574116	SRS4536690	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B1	RESA WT a Am 6h DL B1 AGN000465	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000465\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B1	AGR000594	AGR000594	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000594_R1.fastq.gz	fastq	2077622488.0	27337138.0	AGR000594 R1.fastq.gz	0:76	A:611435382;C:538245690;G:522186419;T:402325956;N:3429041	76		611435382	538245690	522186419	402325956	3429041	SRX5574116	SRS4536690	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00012		1e-05		0.99965		0.58823		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-03-25	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51365	51365	SRR8784176	SRX5574115	SRS4536690	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B1	RESA WT a Am 6h DL B1 AGN000465	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000465\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B1	AGR000592	AGR000592	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000592_R1.fastq.gz	fastq	3782773916.0	49773341.0	AGR000592 R1.fastq.gz	0:76	A:1114409153;C:956769643;G:933746978;T:777498217;N:349925	76		1114409153	956769643	933746978	777498217	349925	SRX5574115	SRS4536690	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.88163		0.07197		0.78376		0.48999		76		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51366	51366	SRR8784177	SRX5574114	SRS4536688	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B2	RESA WT a Am 6h DL B2 AGN000466	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000466\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B2	AGR000595	AGR000595	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000595_R1.fastq.gz	fastq	3181198120.0	41857870.0	AGR000595 R1.fastq.gz	0:76	A:916117551;C:764906267;G:794289368;T:705583699;N:301235	76		916117551	764906267	794289368	705583699	301235	SRX5574114	SRS4536688	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0001		1e-05		0.99969		0.53333		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51367	51367	SRR8784178	SRX5574113	SRS4536688	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B2	RESA WT a Am 6h DL B2 AGN000466	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000466\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B2	AGR000596	AGR000596	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000596_R1.fastq.gz	fastq	379188776.0	4989326.0	AGR000596 R1.fastq.gz	0:76	A:110241873;C:94609649;G:95730118;T:78592018;N:15118	76		110241873	94609649	95730118	78592018	15118	SRX5574113	SRS4536688	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00012		0.0		0.99963		0.55555		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51368	51368	SRR8784179	SRX5574112	SRS4536688	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B2	RESA WT a Am 6h DL B2 AGN000466	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000466\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B2	AGR000597	AGR000597	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000597_R1.fastq.gz	fastq	685459276.0	9019201.0	AGR000597 R1.fastq.gz	0:76	A:197858582;C:171590312;G:173902727;T:142090788;N:16867	76		197858582	171590312	173902727	142090788	16867	SRX5574112	SRS4536688	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00018		4e-05		0.99957		0.31818		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
51369	51369	SRR8784180	SRX5574111	SRS4536688	SRP189389	PRJNA528980	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA	PRJNA528980	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.			RESA WT a Am 6h DL B2	RESA WT a Am 6h DL B2 AGN000466	strain:TU/AB\|age:6\|sex:pooled male and female\|tissue:embryo\|treatment:transcriptome 6h aAm AGN000129 injection alpha am\|molecule:RNA\|sample ref:AGS000444\|replicate ref:AGN000466\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT a Am 6h DL B2	AGR000598	AGR000598	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000598_R1.fastq.gz	fastq	83271604.0	1095679.0	AGR000598 R1.fastq.gz	0:76	A:24099348;C:20368786;G:21051352;T:17745573;N:6545	76		24099348	20368786	21051352	17745573	6545	SRX5574111	SRS4536688	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	8e-05		3e-05		0.99983		0.5		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures

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