metadata: run_metadata: 284 rows where experiment.library_selection = "unspecified", experiment.library_strategy = "RNA-Seq" and tissue

284 rows where experiment.library_selection = "unspecified", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Embryo Imprecise"

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
36406	36406	SRR546819	SRX180749	SRS347211	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 14 somites stage	D. rerio 14 somites embryo	D. rerio 14 somites embryo		RNAseq D. rerio 14 somites embryo	RNAseq D. rerio 14 somites 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_14somites_2.fastq	fastq	2976465520.0	19582010.0	RNAseq D. rerio 14 somites embryo	0:76 1:76	A:747831748;C:733533938;G:754151936;T:738091995;N:2855903	76	76	747831748	733533938	754151936	738091995	2855903	SRX180749	SRS347211	SRA055273	University of Bergen	ZEPROME consortium	2	0.9236	0.91427	0.0861	0.08534	0.7559	0.75528	0.48428	0.47549	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
36407	36407	SRR546818	SRX180748	SRS347209	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 dome/zfs:0000015 stage	D. rerio dome/zfs:0000015 embryo	D. rerio dome/zfs:0000015 embryo		RNAseq D. rerio dome/zfs:0000015 embryo	RNAseq D. rerio dome/zfs:0000015 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_30p_dome_1.fastq	fastq	2359648608.0	15524004.0	RNAseq D. rerio dome/zfs:0000015 embryo	0:76 1:76	A:588562906;C:575605218;G:603310130;T:589755481;N:2414873	76	76	588562906	575605218	603310130	589755481	2414873	SRX180748	SRS347209	SRA055273	University of Bergen	ZEPROME consortium	2	0.89779	0.9222	0.04122	0.0431	0.76609	0.77112	0.49779	0.49305	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36408	36408	SRR546817	SRX180747	SRS358988	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 2 cells stage	D. rerio 2 cells embryo	D. rerio 2 cells embryo		RNAseq D. rerio 2 cells embryo	RNAseq D. rerio 2 cells 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			2799828144.0	18419922.0	RNAseq D. rerio 2 cells embryo	0:76 1:76	A:678251421;C:711410510;G:729905459;T:677312772;N:2947982	76	76	678251421	711410510	729905459	677312772	2947982	SRX180747	SRS358988	SRA055273	University of Bergen	ZEPROME consortium	2	0.9498	0.94704	0.02363	0.02442	0.7988	0.80221	0.48657	0.49361	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Cleavage	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
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
41382	41382	SRR4375306	SRX2226799	SRS1732692	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 WT 8h pA r3 B3	resa AG01070	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B3	AG01070.1	AG01070.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz	fastq fastq	601712368.0	3958634.0	AG01070.1 R2.fastq.gz	0:76 1:76	A:188474921;C:113643606;G:114382568;T:185195364;N:15909	76	76	188474921	113643606	114382568	185195364	15909	SRX2226799	SRS1732692	SRA482696	Yale University\|Genetics	Yale University	2	0.84037	0.84016	0.03493	0.03544	0.97303	0.97252	0.46337	0.47093	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41383	41383	SRR4375305	SRX2226798	SRS1732691	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 WT 8h pA r3 B2	resa AG01069	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B2	AG01069.1	AG01069.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz	fastq fastq	1344477848.0	8845249.0	AG01069.1 R1.fastq.gz	0:76 1:76	A:418545593;C:256422789;G:257715519;T:411760293;N:33654	76	76	418545593	256422789	257715519	411760293	33654	SRX2226798	SRS1732691	SRA482696	Yale University\|Genetics	Yale University	2	0.84542	0.84566	0.03642	0.03588	0.97084	0.97197	0.4739	0.48121	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41384	41384	SRR4375304	SRX2226797	SRS1732690	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 WT 8h pA r3 B1	resa AG01068	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B1	AG01068.1	AG01068.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz	fastq fastq	896200056.0	5896053.0	AG01068.1 R2.fastq.gz	0:76 1:76	A:278768309;C:171161843;G:172303088;T:273944252;N:22564	76	76	278768309	171161843	172303088	273944252	22564	SRX2226797	SRS1732690	SRA482696	Yale University\|Genetics	Yale University	2	0.83862	0.83897	0.0351	0.03585	0.97183	0.97204	0.47364	0.47138	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41385	41385	SRR4375303	SRX2226796	SRS1732689	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 WT 8h L430 pA r3 B3	resa AG01067	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B3	AG01067.1	AG01067.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz	fastq fastq	1799778192.0	11840646.0	AG01067.1 R1.fastq.gz	0:76 1:76	A:561491448;C:342221462;G:343998479;T:552022535;N:44268	76	76	561491448	342221462	343998479	552022535	44268	SRX2226796	SRS1732689	SRA482696	Yale University\|Genetics	Yale University	2	0.84432	0.84397	0.03554	0.03522	0.97224	0.9725	0.46732	0.46922	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41386	41386	SRR4375302	SRX2226795	SRS1732688	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 WT 8h L430 pA r3 B2	resa AG01066	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B2	AG01066.1	AG01066.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz	fastq fastq	1313436864.0	8641032.0	AG01066.1 R2.fastq.gz	0:76 1:76	A:409666264;C:249755645;G:251028600;T:402953610;N:32745	76	76	409666264	249755645	251028600	402953610	32745	SRX2226795	SRS1732688	SRA482696	Yale University\|Genetics	Yale University	2	0.84584	0.84611	0.0349	0.03543	0.97189	0.97175	0.47547	0.48555	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41387	41387	SRR4375301	SRX2226794	SRS1732687	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 WT 8h L430 pA r3 B1	resa AG01065	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B1	AG01065.1	AG01065.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz	fastq fastq	1442385152.0	9489376.0	AG01065.1 R2.fastq.gz	0:76 1:76	A:449362282;C:274879749;G:276626223;T:441480173;N:36725	76	76	449362282	274879749	276626223	441480173	36725	SRX2226794	SRS1732687	SRA482696	Yale University\|Genetics	Yale University	2	0.8417	0.84205	0.03519	0.03559	0.97193	0.97179	0.47697	0.46118	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41388	41388	SRR4375300	SRX2226793	SRS1732685	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 CLIP Ago2 RESA CLIP Ago2 input	resa clip ago2 AG01631	strain:TU/AB\|age:4.7\|dev stage:zfs:0000015\|sex:pooled male and female\|tissue:embryo\|treatment:500UTR flag ago2 crosslink\|molecule:RNA\|selection:5% input before pulldown\|condition:input\|BioSampleModel:Model organism or animal	RESA CLIP Ago2 RESA CLIP Ago2 input	AG01631.1	AG01631.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz	fastq fastq	9864834960.0	64900230.0	AG01631.1 R2.fastq.gz	0:76 1:76	A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520	76	76	2990534603	1958949912	1963153108	2951932817	264520	SRX2226793	SRS1732685	SRA482696	Yale University\|Genetics	Yale University	2	0.83121	0.85078	0.03505	0.0364	0.97171	0.97019	0.46925	0.47246	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41389	41389	SRR4375299	SRX2226779	SRS1732684	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 CLIP Ago2 RESA CLIP Ago2 IP	resa clip ago2 AG01630	strain:TU/AB\|age:4.7\|dev stage:zfs:0000015\|sex:pooled male and female\|tissue:embryo\|treatment:500UTR flag ago2 crosslink\|molecule:RNA\|selection:flag bead pulldown post crosslinking\|condition:Ago2 IP\|BioSampleModel:Model organism or animal	RESA CLIP Ago2 RESA CLIP Ago2 IP	AG01630.1	AG01630.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz	fastq fastq	9348207632.0	61501366.0	AG01630.1 R1.fastq.gz	0:76 1:76	A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848	76	76	2819572908	1871537719	1881735941	2775115216	245848	SRX2226779	SRS1732684	SRA482696	Yale University\|Genetics	Yale University	2	0.80207	0.78648	0.02992	0.02839	0.97885	0.97871	0.49297	0.49107	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41390	41390	SRR4375197	SRX2226727	SRS1732683	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 8h B3	resa AG01086	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B3	AG01086.2	AG01086.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz	fastq fastq	714848400.0	4702950.0	AG01086.2 R2.fastq.gz	0:76 1:76	A:261928616;C:96586565;G:97768464;T:258351392;N:213363	76	76	261928616	96586565	97768464	258351392	213363	SRX2226727	SRS1732683	SRA482696	Yale University\|Genetics	Yale University	2	0.00715	0.00733	0.00046	0.00044	0.99417	0.99435	0.46775	0.42207	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41391	41391	SRR4375176	SRX2226710	SRS1732686	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 WT 64c pA r3 B2	resa AG01061	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 64c pA r3 B2	AG01061.1	AG01061.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz	fastq fastq	724448416.0	4766108.0	AG01061.1 R2.fastq.gz	0:76 1:76	A:224701149;C:138989041;G:139762199;T:220977796;N:18231	76	76	224701149	138989041	139762199	220977796	18231	SRX2226710	SRS1732686	SRA482696	Yale University\|Genetics	Yale University	2	0.84913	0.84756	0.03557	0.03568	0.97153	0.97116	0.47281	0.46157	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-10-06	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41392	41392	SRR4375175	SRX2226709	SRS1732683	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 8h B3	resa AG01086	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B3	AG01086.1	AG01086.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz	fastq fastq	411922128.0	2710014.0	AG01086.1 R1.fastq.gz	0:76 1:76	A:150812258;C:55795177;G:56809368;T:148495332;N:9993	76	76	150812258	55795177	56809368	148495332	9993	SRX2226709	SRS1732683	SRA482696	Yale University\|Genetics	Yale University	2	0.00798	0.00746	0.00062	0.00055	0.99385	0.99399	0.44328	0.47308	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41393	41393	SRR4375146	SRX2226694	SRS1732682	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 8h B2	resa AG01085	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B2	AG01085.2	AG01085.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz	fastq fastq	700337720.0	4607485.0	AG01085.2 R1.fastq.gz	0:76 1:76	A:256568404;C:94627005;G:95783677;T:253149693;N:208941	76	76	256568404	94627005	95783677	253149693	208941	SRX2226694	SRS1732682	SRA482696	Yale University\|Genetics	Yale University	2	0.00733	0.00726	0.00055	0.00048	0.99413	0.99393	0.46893	0.45795	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41394	41394	SRR4375102	SRX2226674	SRS1732682	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 8h B2	resa AG01085	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B2	AG01085.1	AG01085.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz	fastq fastq	409587712.0	2694656.0	AG01085.1 R1.fastq.gz	0:76 1:76	A:149931448;C:55481183;G:56493706;T:147671446;N:9929	76	76	149931448	55481183	56493706	147671446	9929	SRX2226674	SRS1732682	SRA482696	Yale University\|Genetics	Yale University	2	0.0079	0.0078	0.00056	0.0005	0.99366	0.99385	0.42647	0.47214	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41395	41395	SRR4375101	SRX2226673	SRS1732681	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 8h B1	resa AG01084	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B1	AG01084.2	AG01084.2	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz	fastq fastq	396825488.0	2610694.0	AG01084.2 R1.fastq.gz	0:76 1:76	A:145317384;C:53679748;G:54375412;T:143331621;N:121323	76	76	145317384	53679748	54375412	143331621	121323	SRX2226673	SRS1732681	SRA482696	Yale University\|Genetics	Yale University	2	0.0071	0.00673	0.00044	0.00042	0.99417	0.99419	0.44659	0.45357	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41396	41396	SRR4375100	SRX2226672	SRS1732681	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 8h B1	resa AG01084	strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B1	AG01084.1	AG01084.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz	fastq fastq	236514888.0	1556019.0	AG01084.1 R1.fastq.gz	0:76 1:76	A:86560104;C:32062698;G:32664624;T:85221432;N:6030	76	76	86560104	32062698	32664624	85221432	6030	SRX2226672	SRS1732681	SRA482696	Yale University\|Genetics	Yale University	2	0.00756	0.00706	0.00061	0.00064	0.99405	0.99419	0.47228	0.48736	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	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
41402	41402	SRR4375094	SRX2226666	SRS1732677	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 WT 64c pA r3 B1	resa AG01060	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 64c pA r3 B1	AG01060.1	AG01060.1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954	AG01060.1_R1.fastq.gz AG01060.1_R2.fastq.gz	fastq fastq	531097120.0	3494060.0	AG01060.1 R1.fastq.gz	0:76 1:76	A:164891814;C:101739900;G:102440303;T:162011179;N:13924	76	76	164891814	101739900	102440303	162011179	13924	SRX2226666	SRS1732677	SRA482696	Yale University\|Genetics	Yale University	2	0.84523	0.84587	0.03561	0.03503	0.9723	0.97161	0.46204	0.47901	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Cleavage	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
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
43099	43099	SRR5893058	SRX3058787	SRS2404528	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.			mRNA Seq R0 patA WT 64c PatA RPF input B2	mrna seq pata AG01431	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:PatA\|molecule:RNA\|selection:r0\|condition:input\|replicate group:23\|replicate:2\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c PatA RPF input B2	AG01431.1	AG01431.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01431.1_R1.fastq.gz	fastq	935580824.0	12310274.0	AG01431.1 R1.fastq.gz	0:76	A:188726598;C:276745094;G:258235229;T:211815415;N:58488	76		188726598	276745094	258235229	211815415	58488	SRX3058787	SRS2404528	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.89193		0.09644		0.7849		0.69832		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43100	43100	SRR5893059	SRX3058786	SRS2404528	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.			mRNA Seq R0 patA WT 64c PatA RPF input B2	mrna seq pata AG01431	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:PatA\|molecule:RNA\|selection:r0\|condition:input\|replicate group:23\|replicate:2\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c PatA RPF input B2	AG01431.2	AG01431.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01431.2_R1.fastq.gz	fastq	2550535528.0	33559678.0	AG01431.2 R1.fastq.gz	0:76	A:541016830;C:720948568;G:664552003;T:623742439;N:275688	76		541016830	720948568	664552003	623742439	275688	SRX3058786	SRS2404528	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.90466		0.10321		0.77595		0.60561		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43101	43101	SRR5893060	SRX3058785	SRS2404530	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.			mRNA Seq R0 patA WT 64c RPF input B1	mrna seq pata AG01432	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:r0\|condition:input\|replicate group:24\|replicate:1\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c RPF input B1	AG01432.1	AG01432.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01432.1_R1.fastq.gz	fastq	2796444700.0	36795325.0	AG01432.1 R1.fastq.gz	0:76	A:663756831;C:716464328;G:666812843;T:749363967;N:46731	76		663756831	716464328	666812843	749363967	46731	SRX3058785	SRS2404530	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.85828		0.09273		0.75534		0.50507		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43102	43102	SRR5893061	SRX3058784	SRS2404531	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.			mRNA Seq R0 patA WT 64c RPF input B2	mrna seq pata AG01433	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:r0\|condition:input\|replicate group:24\|replicate:2\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c RPF input B2	AG01433.1	AG01433.1	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01433.1_R1.fastq.gz	fastq	3208682532.0	42219507.0	AG01433.1 R1.fastq.gz	0:76	A:715292036;C:869176418;G:807214698;T:816945712;N:53668	76		715292036	869176418	807214698	816945712	53668	SRX3058784	SRS2404531	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.85439		0.09801		0.76597		0.58538		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43115	43115	SRR5893082	SRX3058763	SRS2404539	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.			mRNA Seq R0 patA WT 64c PatA RPF input B1	mrna seq pata AG01430	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:PatA\|molecule:RNA\|selection:r0\|condition:input\|replicate group:23\|replicate:1\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c PatA RPF input B1	AG01430.2	AG01430.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01430.2_R1.fastq.gz	fastq	3133028560.0	41224060.0	AG01430.2 R1.fastq.gz	0:76	A:672361176;C:875054552;G:808035984;T:777238497;N:338351	76		672361176	875054552	808035984	777238497	338351	SRX3058763	SRS2404539	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.88898		0.09238		0.77234		0.6234		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43116	43116	SRR5893083	SRX3058762	SRS2404539	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.			mRNA Seq R0 patA WT 64c PatA RPF input B1	mrna seq pata AG01430	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:PatA\|molecule:RNA\|selection:r0\|condition:input\|replicate group:23\|replicate:1\|BioSampleModel:Model organism or animal	mRNA Seq R0 patA WT 64c PatA RPF input B1	AG01430.1	AG01430.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782	AG01430.1_R1.fastq.gz	fastq	898114724.0	11817299.0	AG01430.1 R1.fastq.gz	0:76	A:187456862;C:260421633;G:242938837;T:207239930;N:57462	76		187456862	260421633	242938837	207239930	57462	SRX3058762	SRS2404539	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87315		0.08685		0.78117		0.65305		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2017-08-03	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
46211	46211	SRR6477199	SRX3567065	SRS2838997	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 Bud13 Bud13 Sibling 30h	RNAseq Bud13 Bud13 Sib 30h AG01145	strain:TU/AB\|age:30.0\|dev stage:30h\|sex:pooled male and female\|tissue:embryo\|genotype:+/?\|molecule:mRNA\|selection:pA\|replicate group:2\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq Bud13 Bud13 Sibling 30h	AG01145.2	AG01145.2	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP129892	AG01145.2_R2.fastq.gz AG01145.2_R1.fastq.gz	fastq fastq	12323940056.0	81078553.0	AG01145.2 R1.fastq.gz	0:76 1:76	A:3425803431;C:2777524766;G:2722925333;T:3380952969;N:16733557	76	76	3425803431	2777524766	2722925333	3380952969	16733557	SRX3567065	SRS2838997	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.94345	0.94709	0.12521	0.12335	0.69165	0.69475	0.4685	0.47082	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-01-17	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
46212	46212	SRR6477200	SRX3567064	SRS2838996	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 Bud13 Bud13 KO 30h	RNAseq Bud13 Bud13 KO 30h AG01144	strain:TU/AB\|age:30.0\|dev stage:30h\|sex:pooled male and female\|tissue:embryo\|genotype: / \|molecule:mRNA\|selection:pA\|replicate group:1\|replicate:1\|BioSampleModel:Model organism or animal	RNAseq Bud13 Bud13 KO 30h	AG01144.2	AG01144.2	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP129892	AG01144.2_R1.fastq.gz AG01144.2_R2.fastq.gz	fastq fastq	12242377920.0	80541960.0	AG01144.2 R1.fastq.gz	0:76 1:76	A:3501235324;C:2524126832;G:2520934401;T:3679154562;N:16926801	76	76	3501235324	2524126832	2520934401	3679154562	16926801	SRX3567064	SRS2838996	SRA647342	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93874	0.93814	0.2229	0.17671	0.71102	0.71234	0.48631	0.48352	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-23	Pharyngula	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
48356	48356	SRR5893042	SRX3058803	SRS2404515	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 64c R0 B2	dev timecourse AG00671	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:4\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 64c R0 B2	AG00671.2	AG00671.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00671.2_R1.fastq.gz AG00671.2_R2.fastq.gz	fastq fastq	3401007752.0	22375051.0	AG00671.2 R1.fastq.gz	0:76 1:76	A:761237295;C:934945811;G:938845233;T:765218661;N:760752	76	76	761237295	934945811	938845233	765218661	760752	SRX3058803	SRS2404515	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.71455	0.77271	0.06416	0.06853	0.77017	0.77189	0.48808	0.48936	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48357	48357	SRR5893043	SRX3058802	SRS2404516	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 1Kc R0 B1	dev timecourse AG00674	strain:TU/AB\|age:3.0\|dev stage:1Kc\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:5\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1Kc R0 B1	AG00674.1	AG00674.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00674.1_R1.fastq.gz AG00674.1_R2.fastq.gz	fastq fastq	2778354192.0	18278646.0	AG00674.1 R1.fastq.gz	0:76 1:76	A:714760759;C:677314739;G:673805073;T:706600617;N:5873004	76	76	714760759	677314739	673805073	706600617	5873004	SRX3058802	SRS2404516	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.86999	0.85982	0.06795	0.06797	0.7625	0.7615	0.47908	0.47887	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48358	48358	SRR5893044	SRX3058801	SRS2404514	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 64c pA B1	dev timecourse AG00644	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:1\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 64c pA B1	AG00644.1	AG00644.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00644.1_R1.fastq.gz AG00644.1_R2.fastq.gz	fastq fastq	2457941384.0	16170667.0	AG00644.1 R2.fastq.gz	0:76 1:76	A:655179090;C:570607586;G:571155579;T:658430586;N:2568543	76	76	655179090	570607586	571155579	658430586	2568543	SRX3058801	SRS2404514	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.94406	0.94075	0.02483	0.02699	0.76936	0.76966	0.48505	0.48646	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48359	48359	SRR5893045	SRX3058800	SRS2404517	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 64c pA B2	dev timecourse AG00645	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:1\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 64c pA B2	AG00645.1	AG00645.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00645.1_R1.fastq.gz AG00645.1_R2.fastq.gz	fastq fastq	2643787680.0	17393340.0	AG00645.1 R1.fastq.gz	0:76 1:76	A:704257377;C:614686679;G:614950025;T:707119985;N:2773614	76	76	704257377	614686679	614950025	707119985	2773614	SRX3058800	SRS2404517	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93726	0.94194	0.02686	0.02578	0.76834	0.76893	0.48339	0.47898	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48360	48360	SRR5893046	SRX3058799	SRS2404519	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT sphere pA B1	dev timecourse AG00652	strain:TU/AB\|age:4.0\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:2\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT sphere pA B1	AG00652.1	AG00652.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00652.1_R1.fastq.gz AG00652.1_R2.fastq.gz	fastq fastq	2249814472.0	14801411.0	AG00652.1 R2.fastq.gz	0:76 1:76	A:601647003;C:522830587;G:520544682;T:602476586;N:2315614	76	76	601647003	522830587	520544682	602476586	2315614	SRX3058799	SRS2404519	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.94297	0.93993	0.04239	0.0447	0.74627	0.74651	0.48492	0.48304	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2017-08-03	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48361	48361	SRR5893047	SRX3058798	SRS2404518	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT sphere pA B2	dev timecourse AG00653	strain:TU/AB\|age:4.0\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:2\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT sphere pA B2	AG00653.1	AG00653.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00653.1_R1.fastq.gz AG00653.1_R2.fastq.gz	fastq fastq	2426358520.0	15962885.0	AG00653.1 R2.fastq.gz	0:76 1:76	A:652817175;C:559502193;G:558238114;T:653277750;N:2523288	76	76	652817175	559502193	558238114	653277750	2523288	SRX3058798	SRS2404518	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93982	0.9342	0.0439	0.04618	0.74823	0.74777	0.48614	0.48263	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48362	48362	SRR5893048	SRX3058797	SRS2404520	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT shield pA B1	dev timecourse AG00658	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:3\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT shield pA B1	AG00658.1	AG00658.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00658.1_R2.fastq.gz AG00658.1_R1.fastq.gz	fastq fastq	2368759640.0	15583945.0	AG00658.1 R2.fastq.gz	0:76 1:76	A:643327175;C:540895938;G:540699719;T:641357257;N:2479551	76	76	643327175	540895938	540699719	641357257	2479551	SRX3058797	SRS2404520	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.89596	0.89407	0.07479	0.07678	0.76004	0.7595	0.48733	0.48807	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48363	48363	SRR5893049	SRX3058796	SRS2404521	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT shield pA B2	dev timecourse AG00659	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|replicate group:3\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT shield pA B2	AG00659.1	AG00659.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00659.1_R1.fastq.gz AG00659.1_R2.fastq.gz	fastq fastq	2038811568.0	13413234.0	AG00659.1 R2.fastq.gz	0:76 1:76	A:558819941;C:458698081;G:460805877;T:558399462;N:2088207	76	76	558819941	458698081	460805877	558399462	2088207	SRX3058796	SRS2404521	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.92967	0.92885	0.0788	0.08121	0.75661	0.75631	0.49269	0.49182	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2017-08-03	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48364	48364	SRR5893050	SRX3058795	SRS2404522	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 64c R0 B1	dev timecourse AG00670	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:4\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 64c R0 B1	AG00670.1	AG00670.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00670.1_R1.fastq.gz AG00670.1_R2.fastq.gz	fastq fastq	2692216248.0	17711949.0	AG00670.1 R1.fastq.gz	0:76 1:76	A:681268366;C:669533858;G:662344502;T:673374314;N:5695208	76	76	681268366	669533858	662344502	673374314	5695208	SRX3058795	SRS2404522	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.858	0.83961	0.06542	0.06545	0.76623	0.76463	0.47797	0.48023	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48365	48365	SRR5893051	SRX3058794	SRS2404515	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 64c R0 B2	dev timecourse AG00671	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:4\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 64c R0 B2	AG00671.1	AG00671.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00671.1_R1.fastq.gz AG00671.1_R2.fastq.gz	fastq fastq	1411014176.0	9282988.0	AG00671.1 R2.fastq.gz	0:76 1:76	A:356427462;C:351288483;G:348446516;T:351946038;N:2905677	76	76	356427462	351288483	348446516	351946038	2905677	SRX3058794	SRS2404515	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.83575	0.85161	0.06672	0.06526	0.76416	0.76615	0.48088	0.47816	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48366	48366	SRR5893064	SRX3058781	SRS2404533	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 64c R0 B1	dev timecourse AG00728	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:10\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 64c R0 B1	AG00728.1	AG00728.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00728.1_R1.fastq.gz AG00728.1_R2.fastq.gz	fastq fastq	2789035232.0	18348916.0	AG00728.1 R1.fastq.gz	0:76 1:76	A:746104532;C:614735198;G:636481842;T:785596249;N:6117411	76	76	746104532	614735198	636481842	785596249	6117411	SRX3058781	SRS2404533	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.51926	0.49218	0.08229	0.0936	0.80744	0.8103	0.48989	0.48658	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48367	48367	SRR5893065	SRX3058780	SRS2404535	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am shield pA B2	dev timecourse AG00701	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:9\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am shield pA B2	AG00701.1	AG00701.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00701.1_R1.fastq.gz AG00701.1_R2.fastq.gz	fastq fastq	2611389944.0	17180197.0	AG00701.1 R1.fastq.gz	0:76 1:76	A:696886025;C:607737206;G:605609129;T:699045963;N:2111621	76	76	696886025	607737206	605609129	699045963	2111621	SRX3058780	SRS2404535	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.9089	0.91353	0.03824	0.03668	0.78261	0.78293	0.49562	0.49348	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48368	48368	SRR5893066	SRX3058779	SRS2404534	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 1Kc R0 B1	dev timecourse AG00729	strain:TU/AB\|age:3.0\|dev stage:1Kc\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:11\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 1Kc R0 B1	AG00729.1	AG00729.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00729.1_R1.fastq.gz AG00729.1_R2.fastq.gz	fastq fastq	1890136872.0	12435111.0	AG00729.1 R1.fastq.gz	0:76 1:76	A:533950687;C:392378762;G:409763231;T:549817692;N:4226500	76	76	533950687	392378762	409763231	549817692	4226500	SRX3058779	SRS2404534	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.63533	0.59715	0.26221	0.24377	0.76924	0.77303	0.49119	0.4915	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48369	48369	SRR5893067	SRX3058778	SRS2404533	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 64c R0 B1	dev timecourse AG00728	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:10\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 64c R0 B1	AG00728.2	AG00728.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00728.2_R1.fastq.gz AG00728.2_R2.fastq.gz	fastq fastq	3094128568.0	20356109.0	AG00728.2 R2.fastq.gz	0:76 1:76	A:788885030;C:743206390;G:779938637;T:769114909;N:12983602	76	76	788885030	743206390	779938637	769114909	12983602	SRX3058778	SRS2404533	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.45295	0.45728	0.06671	0.06598	0.81389	0.81213	0.48974	0.48842	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48370	48370	SRR5893068	SRX3058777	SRS2404536	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 shield R0 B1	dev timecourse AG00730	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:12\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 shield R0 B1	AG00730.1	AG00730.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00730.1_R1.fastq.gz AG00730.1_R2.fastq.gz	fastq fastq	788630112.0	5188356.0	AG00730.1 R1.fastq.gz	0:76 1:76	A:241944426;C:145730020;G:152521090;T:246715939;N:1718637	76	76	241944426	145730020	152521090	246715939	1718637	SRX3058777	SRS2404536	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.72997	0.66601	0.51477	0.46195	0.7611	0.77027	0.48262	0.48514	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48371	48371	SRR5893069	SRX3058776	SRS2404534	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 1Kc R0 B1	dev timecourse AG00729	strain:TU/AB\|age:3.0\|dev stage:1Kc\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:11\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 1Kc R0 B1	AG00729.2	AG00729.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00729.2_R1.fastq.gz AG00729.2_R2.fastq.gz	fastq fastq	2313466600.0	15220175.0	AG00729.2 R1.fastq.gz	0:76 1:76	A:629795330;C:513868215;G:540304279;T:629131946;N:366830	76	76	629795330	513868215	540304279	629131946	366830	SRX3058776	SRS2404534	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.58985	0.55361	0.25806	0.21955	0.76593	0.7791	0.49969	0.49044	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48372	48372	SRR5893070	SRX3058775	SRS2404536	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 shield R0 B1	dev timecourse AG00730	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:12\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 shield R0 B1	AG00730.3	AG00730.3	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00730.3_R1.fastq.gz AG00730.3_R2.fastq.gz	fastq fastq	2381566704.0	15668202.0	AG00730.3 R2.fastq.gz	0:76 1:76	A:699742976;C:480758524;G:501871756;T:694897427;N:4296021	76	76	699742976	480758524	501871756	694897427	4296021	SRX3058775	SRS2404536	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.64984	0.69686	0.44721	0.49461	0.77575	0.7558	0.49124	0.49296	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48373	48373	SRR5893071	SRX3058774	SRS2404536	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT TinyLNA430 shield R0 B1	dev timecourse AG00730	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:tinyLNA miR 430\|molecule:RNA\|selection:r0\|replicate group:12\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT TinyLNA430 shield R0 B1	AG00730.2	AG00730.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00730.2_R1.fastq.gz AG00730.2_R2.fastq.gz	fastq fastq	2758536584.0	18148267.0	AG00730.2 R2.fastq.gz	0:76 1:76	A:819274018;C:547358767;G:578250069;T:813046584;N:607146	76	76	819274018	547358767	578250069	813046584	607146	SRX3058774	SRS2404536	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.63895	0.70578	0.44175	0.50387	0.76844	0.74988	0.49353	0.49135	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48374	48374	SRR5893161	SRX3058684	SRS2404573	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am sphere pA B2	dev timecourse AG00699	strain:TU/AB\|age:4.0\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:8\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am sphere pA B2	AG00699.1	AG00699.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00699.1_R1.fastq.gz AG00699.1_R2.fastq.gz	fastq fastq	3068083672.0	20184761.0	AG00699.1 R2.fastq.gz	0:76 1:76	A:815949630;C:716718414;G:714252482;T:818688450;N:2474696	76	76	815949630	716718414	714252482	818688450	2474696	SRX3058684	SRS2404573	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93448	0.93065	0.02663	0.02862	0.76577	0.76597	0.48311	0.48106	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48375	48375	SRR5893162	SRX3058683	SRS2404571	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am shield pA B1	dev timecourse AG00700	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:9\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am shield pA B1	AG00700.1	AG00700.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00700.1_R1.fastq.gz AG00700.1_R2.fastq.gz	fastq fastq	2276298800.0	14975650.0	AG00700.1 R1.fastq.gz	0:76 1:76	A:608754452;C:529104329;G:527812421;T:608782771;N:1844827	76	76	608754452	529104329	527812421	608782771	1844827	SRX3058683	SRS2404571	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.91533	0.91935	0.03891	0.03686	0.78289	0.78281	0.49374	0.49427	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48376	48376	SRR5893163	SRX3058682	SRS2404574	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT shield R0 B2	dev timecourse AG00685	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:6\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT shield R0 B2	AG00685.2	AG00685.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00685.2_R1.fastq.gz AG00685.2_R2.fastq.gz	fastq fastq	1680110568.0	11053359.0	AG00685.2 R2.fastq.gz	0:76 1:76	A:429590606;C:407853081;G:410551734;T:431833883;N:281264	76	76	429590606	407853081	410551734	431833883	281264	SRX3058682	SRS2404574	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.80758	0.77739	0.2587	0.25273	0.75162	0.75012	0.49289	0.48814	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48377	48377	SRR5893164	SRX3058681	SRS2404572	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am 64c pA B1	dev timecourse AG00692	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:7\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 64c pA B1	AG00692.1	AG00692.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00692.1_R1.fastq.gz AG00692.1_R2.fastq.gz	fastq fastq	1769692528.0	11642714.0	AG00692.1 R1.fastq.gz	0:76 1:76	A:473892393;C:411257494;G:409923797;T:473090107;N:1528737	76	76	473892393	411257494	409923797	473090107	1528737	SRX3058681	SRS2404572	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.91805	0.92435	0.02685	0.02528	0.76903	0.76893	0.49124	0.48516	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48378	48378	SRR5893165	SRX3058680	SRS2404575	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am 64c pA B2	dev timecourse AG00693	strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:7\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 64c pA B2	AG00693.1	AG00693.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00693.1_R1.fastq.gz AG00693.1_R2.fastq.gz	fastq fastq	2431950600.0	15999675.0	AG00693.1 R1.fastq.gz	0:76 1:76	A:649992656;C:564963471;G:562148972;T:652726417;N:2119084	76	76	649992656	564963471	562148972	652726417	2119084	SRX3058680	SRS2404575	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.92915	0.93349	0.02655	0.02536	0.76469	0.76556	0.48791	0.48893	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
48379	48379	SRR5893166	SRX3058679	SRS2404576	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT a Am sphere pA B1	dev timecourse AG00698	strain:TU/AB\|age:4.0\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|replicate group:8\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am sphere pA B1	AG00698.1	AG00698.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00698.1_R1.fastq.gz AG00698.1_R2.fastq.gz	fastq fastq	3080491584.0	20266392.0	AG00698.1 R2.fastq.gz	0:76 1:76	A:820145004;C:719352396;G:717040476;T:821459264;N:2494444	76	76	820145004	719352396	717040476	821459264	2494444	SRX3058679	SRS2404576	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93863	0.93287	0.02829	0.03003	0.76674	0.76613	0.48947	0.48528	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48380	48380	SRR5893167	SRX3058678	SRS2404577	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 1Kc R0 B2	dev timecourse AG00675	strain:TU/AB\|age:3.0\|dev stage:1Kc\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:5\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1Kc R0 B2	AG00675.1	AG00675.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00675.1_R1.fastq.gz AG00675.1_R2.fastq.gz	fastq fastq	2036894544.0	13400622.0	AG00675.1 R1.fastq.gz	0:76 1:76	A:518808025;C:503536266;G:498902325;T:511311573;N:4336355	76	76	518808025	503536266	498902325	511311573	4336355	SRX3058678	SRS2404577	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.8614	0.84624	0.07306	0.07361	0.76621	0.7651	0.48141	0.47999	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48381	48381	SRR5893168	SRX3058677	SRS2404577	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 1Kc R0 B2	dev timecourse AG00675	strain:TU/AB\|age:3.0\|dev stage:1Kc\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:5\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1Kc R0 B2	AG00675.2	AG00675.2	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00675.2_R1.fastq.gz AG00675.2_R2.fastq.gz	fastq fastq	2783867992.0	18314921.0	AG00675.2 R1.fastq.gz	0:76 1:76	A:638343367;C:750975688;G:753870541;T:640053360;N:625036	76	76	638343367	750975688	753870541	640053360	625036	SRX3058677	SRS2404577	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.73502	0.78624	0.07089	0.0748	0.76865	0.76999	0.48242	0.48382	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Blastula	Embryo	Embryo Imprecise	All anatomical structures
48382	48382	SRR5893169	SRX3058676	SRS2404578	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT shield R0 B1	dev timecourse AG00684	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:6\|replicate:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT shield R0 B1	AG00684.1	AG00684.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00684.1_R2.fastq.gz AG00684.1_R1.fastq.gz	fastq fastq	2226499040.0	14648020.0	AG00684.1 R1.fastq.gz	0:76 1:76	A:602558683;C:513781901;G:511035245;T:594547415;N:4575796	76	76	602558683	513781901	511035245	594547415	4575796	SRX3058676	SRS2404578	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.8496	0.84272	0.25441	0.24624	0.7501	0.74838	0.47046	0.47693	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48383	48383	SRR5893170	SRX3058675	SRS2404574	SRP149556	PRJNA473824	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq	PRJNA473824	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.This is the developmental mRNA seq timecourse part of the study.			Developmental timecourse WT shield R0 B2	dev timecourse AG00685	strain:TU/AB\|age:6.0\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|replicate group:6\|replicate:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT shield R0 B2	AG00685.1	AG00685.1	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP149556	AG00685.1_R2.fastq.gz AG00685.1_R1.fastq.gz	fastq fastq	2296708448.0	15109924.0	AG00685.1 R1.fastq.gz	0:76 1:76	A:629149868;C:520713186;G:520261374;T:621870139;N:4713881	76	76	629149868	520713186	520261374	621870139	4713881	SRX3058675	SRS2404574	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84968	0.84234	0.28684	0.27563	0.74957	0.74667	0.47755	0.4838	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51152	51152	SRR8552544	SRX5354346	SRS4345564	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 WT 2h R0	mRNA seq WT 2h R0 AGN001827	strain:TU/AB\|age:2.0\|dev stage:64 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS001459\|replicate ref:AGN001827\|replicate order:1\|BioSampleModel:Model organism or animal	mRNA seq WT 2h R0	AGR002489	AGR002489	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP184786	AGR002489_R1.fastq.gz	fastq	1915424276.0	25202951.0	AGR002489 R1.fastq.gz	0:76	A:427998951;C:502027263;G:488957899;T:496384297;N:55866	76		427998951	502027263	488957899	496384297	55866	SRX5354346	SRS4345564	SRA847217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.83803		0.08509		0.75753		0.47975		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-02-08	Cleavage	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
51154	51154	SRR8552546	SRX5354344	SRS4345562	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 WT 4h R0	mRNA seq WT 4h R0 AGN001743	strain:TU/AB\|age:4.0\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|condition:untreated\|sample ref:AGS001389\|replicate ref:AGN001743\|replicate order:1\|BioSampleModel:Model organism or animal	mRNA seq WT 4h R0	AGR002398	AGR002398	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP184786	AGR002398_R1.fastq.gz	fastq	1304401604.0	17163179.0	AGR002398 R1.fastq.gz	0:76	A:248973263;C:385894356;G:377042802;T:292460281;N:30902	76		248973263	385894356	377042802	292460281	30902	SRX5354344	SRS4345562	SRA847217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.82485		0.15823		0.78847		0.75023		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-06-12	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51332	51332	SRR8784143	SRX5574148	SRS4536708	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 r2 B2	RESA WT 6h r2 B2 AGN000587	strain:TU/AB\|age:6\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000532\|replicate ref:AGN000587\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h r2 B2	AGR000770	AGR000770	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000770_R1.fastq.gz AGR000770_R2.fastq.gz	fastq fastq	710612768.0	4675084.0	AGR000770 R1.fastq.gz	0:76 1:76	A:216034520;C:140249508;G:140825200;T:212576797;N:926743	76	76	216034520	140249508	140825200	212576797	926743	SRX5574148	SRS4536708	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84791	0.85232	0.03648	0.0373	0.96992	0.96982	0.47482	0.48015	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51333	51333	SRR8784144	SRX5574147	SRS4536708	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 r2 B2	RESA WT 6h r2 B2 AGN000587	strain:TU/AB\|age:6\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000532\|replicate ref:AGN000587\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 6h r2 B2	AGR000769	AGR000769	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000769_R1.fastq.gz AGR000769_R2.fastq.gz	fastq fastq	211548888.0	1391769.0	AGR000769 R1.fastq.gz	0:76 1:76	A:64102332;C:41963002;G:42116026;T:62997625;N:369903	76	76	64102332	41963002	42116026	62997625	369903	SRX5574147	SRS4536708	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84057	0.84101	0.03626	0.03615	0.96903	0.96924	0.47894	0.48212	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	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
51335	51335	SRR8784146	SRX5574145	SRS4536706	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 r2 B3	RESA WT 6h r2 B3 AGN000591	strain:TU/AB\|age:6\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000532\|replicate ref:AGN000591\|replicate order:3\|BioSampleModel:Model organism or animal	RESA WT 6h r2 B3	AGR000771	AGR000771	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000771_R1.fastq.gz AGR000771_R2.fastq.gz	fastq fastq	857903504.0	5644102.0	AGR000771 R1.fastq.gz	0:76 1:76	A:261246476;C:168915312;G:169170702;T:257095534;N:1475480	76	76	261246476	168915312	169170702	257095534	1475480	SRX5574145	SRS4536706	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84499	0.84594	0.0361	0.03624	0.96924	0.96954	0.48999	0.48378	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51338	51338	SRR8784149	SRX5574142	SRS4536705	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 r2 B1	RESA WT 6h r2 B1 AGN000582	strain:TU/AB\|age:6\|dev stage:shield\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000532\|replicate ref:AGN000582\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT 6h r2 B1	AGR000768	AGR000768	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000768_R1.fastq.gz AGR000768_R2.fastq.gz	fastq fastq	970151856.0	6382578.0	AGR000768 R1.fastq.gz	0:76 1:76	A:294386849;C:192114485;G:192378258;T:289576859;N:1695405	76	76	294386849	192114485	192378258	289576859	1695405	SRX5574142	SRS4536705	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84582	0.84496	0.0368	0.03617	0.96857	0.96861	0.47723	0.46086	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	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
51352	51352	SRR8784163	SRX5574128	SRS4536699	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 32c r2 B3	RESA WT 32c r2 B3 AGN000590	strain:TU/AB\|age:2\|dev stage:32 cell\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000535\|replicate ref:AGN000590\|replicate order:3\|BioSampleModel:Model organism or animal	RESA WT 32c r2 B3	AGR000783	AGR000783	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000783_R1.fastq.gz AGR000783_R2.fastq.gz	fastq fastq	1617867480.0	10643865.0	AGR000783 R1.fastq.gz	0:76 1:76	A:487377678;C:324054887;G:324329007;T:479297973;N:2807935	76	76	487377678	324054887	324329007	479297973	2807935	SRX5574128	SRS4536699	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85088	0.85003	0.03672	0.03663	0.96771	0.96822	0.47246	0.48068	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51353	51353	SRR8784164	SRX5574127	SRS4536698	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 8h a Am pA r3 B1	RESA WT 8h a Am pA r3 B1 AGN001062	strain:TU/AB\|age:8\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|selection:pA\|sample ref:AGS000941\|replicate ref:AGN001062\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT 8h a Am pA r3 B1	AGR001457	AGR001457	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR001457_R1.fastq.gz AGR001457_R2.fastq.gz	fastq fastq	1091406664.0	7180307.0	AGR001457 R1.fastq.gz	0:76 1:76	A:338277626;C:209601360;G:211052818;T:332448031;N:26829	76	76	338277626	209601360	211052818	332448031	26829	SRX5574127	SRS4536698	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.843	0.84316	0.03591	0.03493	0.97133	0.97074	0.47855	0.47491	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	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
51357	51357	SRR8784168	SRX5574123	SRS4536695	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 32c r2 B1	RESA WT 32c r2 B1 AGN000585	strain:TU/AB\|age:2\|dev stage:32 cell\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000535\|replicate ref:AGN000585\|replicate order:1\|BioSampleModel:Model organism or animal	RESA WT 32c r2 B1	AGR000780	AGR000780	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000780_R1.fastq.gz AGR000780_R2.fastq.gz	fastq fastq	1681768888.0	11064269.0	AGR000780 R1.fastq.gz	0:76 1:76	A:505494052;C:337906595;G:338065121;T:497364873;N:2938247	76	76	505494052	337906595	338065121	497364873	2938247	SRX5574123	SRS4536695	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85285	0.85386	0.03748	0.03778	0.96779	0.9681	0.47501	0.47905	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	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
51370	51370	SRR8784181	SRX5574110	SRS4536687	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 32c r2 B2	RESA WT 32c r2 B2 AGN000586	strain:TU/AB\|age:2\|dev stage:32 cell\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000535\|replicate ref:AGN000586\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 32c r2 B2	AGR000781	AGR000781	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000781_R1.fastq.gz AGR000781_R2.fastq.gz	fastq fastq	744470920.0	4897835.0	AGR000781 R1.fastq.gz	0:76 1:76	A:223413105;C:150069118;G:150396751;T:219294649;N:1297297	76	76	223413105	150069118	150396751	219294649	1297297	SRX5574110	SRS4536687	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84699	0.84827	0.03648	0.03659	0.96771	0.96788	0.4851	0.48316	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51371	51371	SRR8784182	SRX5574109	SRS4536687	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 32c r2 B2	RESA WT 32c r2 B2 AGN000586	strain:TU/AB\|age:2\|dev stage:32 cell\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|sample ref:AGS000535\|replicate ref:AGN000586\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 32c r2 B2	AGR000782	AGR000782	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR000782_R1.fastq.gz AGR000782_R2.fastq.gz	fastq fastq	2728809336.0	17952693.0	AGR000782 R1.fastq.gz	0:76 1:76	A:820893743;C:547298890;G:549853268;T:807123376;N:3640059	76	76	820893743	547298890	549853268	807123376	3640059	SRX5574109	SRS4536687	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.85693	0.85768	0.03694	0.03654	0.96749	0.9681	0.47802	0.47988	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51372	51372	SRR8784183	SRX5574108	SRS4536689	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 8h a Am pA r3 B3	RESA WT 8h a Am pA r3 B3 AGN001064	strain:TU/AB\|age:8\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|selection:pA\|sample ref:AGS000941\|replicate ref:AGN001064\|replicate order:3\|BioSampleModel:Model organism or animal	RESA WT 8h a Am pA r3 B3	AGR001459	AGR001459	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR001459_R1.fastq.gz AGR001459_R2.fastq.gz	fastq fastq	1466122688.0	9645544.0	AGR001459 R1.fastq.gz	0:76 1:76	A:455341747;C:280749005;G:282302377;T:447692059;N:37500	76	76	455341747	280749005	282302377	447692059	37500	SRX5574108	SRS4536689	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84266	0.84348	0.03662	0.0361	0.97232	0.97218	0.46974	0.47375	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51373	51373	SRR8784184	SRX5574107	SRS4536686	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 8h a Am pA r3 B2	RESA WT 8h a Am pA r3 B2 AGN001063	strain:TU/AB\|age:8\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr alpha am\|molecule:RNA\|selection:pA\|sample ref:AGS000941\|replicate ref:AGN001063\|replicate order:2\|BioSampleModel:Model organism or animal	RESA WT 8h a Am pA r3 B2	AGR001458	AGR001458	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189389	AGR001458_R1.fastq.gz AGR001458_R2.fastq.gz	fastq fastq	728165424.0	4790562.0	AGR001458 R1.fastq.gz	0:76 1:76	A:225801650;C:139760608;G:140579216;T:222005064;N:18886	76	76	225801650	139760608	140579216	222005064	18886	SRX5574107	SRS4536686	SRA865803	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84582	0.845	0.03593	0.03495	0.9713	0.97189	0.47034	0.47028	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51615	51615	SRR8788626	SRX5578497	SRS4540274	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 4c R0 B1	Developmental timecourse WT 4c R0 B1 AGN000666	strain:TU/AB\|age:1.0\|dev stage:4 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000585\|replicate ref:AGN000666\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 4c R0 B1	AGR000861	AGR000861	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000861_R2.fastq.gz AGR000861_R1.fastq.gz	fastq fastq	2888554344.0	19003647.0	AGR000861 R1.fastq.gz	0:76 1:76	A:673571075;C:760569181;G:775244536;T:678822696;N:346856	76	76	673571075	760569181	775244536	678822696	346856	SRX5578497	SRS4540274	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.75836	0.8073	0.07453	0.07791	0.76566	0.76745	0.48548	0.48444	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51616	51616	SRR8788627	SRX5578496	SRS4540274	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 4c R0 B1	Developmental timecourse WT 4c R0 B1 AGN000666	strain:TU/AB\|age:1.0\|dev stage:4 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000585\|replicate ref:AGN000666\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 4c R0 B1	AGR000860	AGR000860	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000860_R1.fastq.gz AGR000860_R2.fastq.gz	fastq fastq	1684739272.0	11083811.0	AGR000860 R1.fastq.gz	0:76 1:76	A:429432817;C:412139047;G:414231556;T:426015778;N:2920074	76	76	429432817	412139047	414231556	426015778	2920074	SRX5578496	SRS4540274	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.86855	0.85707	0.07231	0.07348	0.76187	0.76049	0.47575	0.48049	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51617	51617	SRR8788628	SRX5578495	SRS4540273	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 2c R0 B2	Developmental timecourse WT 2c R0 B2 AGN000665	strain:TU/AB\|age:0.75\|dev stage:2 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000584\|replicate ref:AGN000665\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 2c R0 B2	AGR000859	AGR000859	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000859_R1.fastq.gz AGR000859_R2.fastq.gz	fastq fastq	2132978912.0	14032756.0	AGR000859 R1.fastq.gz	0:76 1:76	A:453107239;C:603446010;G:622466425;T:453479291;N:479947	76	76	453107239	603446010	622466425	453479291	479947	SRX5578495	SRS4540273	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.65481	0.69653	0.06284	0.06531	0.77256	0.774	0.48127	0.47849	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51618	51618	SRR8788629	SRX5578494	SRS4540273	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 2c R0 B2	Developmental timecourse WT 2c R0 B2 AGN000665	strain:TU/AB\|age:0.75\|dev stage:2 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000584\|replicate ref:AGN000665\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 2c R0 B2	AGR000858	AGR000858	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000858_R1.fastq.gz AGR000858_R2.fastq.gz	fastq fastq	1559318904.0	10258677.0	AGR000858 R1.fastq.gz	0:76 1:76	A:384695273;C:394725604;G:397400659;T:379794145;N:2703223	76	76	384695273	394725604	397400659	379794145	2703223	SRX5578494	SRS4540273	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.84496	0.8225	0.07114	0.07094	0.76702	0.76542	0.47578	0.47713	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51619	51619	SRR8788630	SRX5578493	SRS4540270	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 2c R0 B1	Developmental timecourse WT 2c R0 B1 AGN000664	strain:TU/AB\|age:0.75\|dev stage:2 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000584\|replicate ref:AGN000664\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 2c R0 B1	AGR000857	AGR000857	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000857_R2.fastq.gz AGR000857_R1.fastq.gz	fastq fastq	2376722312.0	15636331.0	AGR000857 R1.fastq.gz	0:76 1:76	A:500785483;C:677939328;G:697249507;T:500463235;N:284759	76	76	500785483	677939328	697249507	500463235	284759	SRX5578493	SRS4540270	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.62459	0.66696	0.05928	0.06311	0.77561	0.77646	0.48626	0.48501	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51620	51620	SRR8788631	SRX5578492	SRS4540270	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	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 developmental mRNA seq timecourse part of the study.			Developmental timecourse WT 2c R0 B1	Developmental timecourse WT 2c R0 B1 AGN000664	strain:TU/AB\|age:0.75\|dev stage:2 cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000584\|replicate ref:AGN000664\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 2c R0 B1	AGR000856	AGR000856	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP189512	AGR000856_R1.fastq.gz AGR000856_R2.fastq.gz	fastq fastq	1840525744.0	12108722.0	AGR000856 R1.fastq.gz	0:76 1:76	A:454686905;C:466397166;G:467734327;T:448518702;N:3188644	76	76	454686905	466397166	467734327	448518702	3188644	SRX5578492	SRS4540270	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.82233	0.79883	0.06922	0.0685	0.76731	0.76658	0.47465	0.48079	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Cleavage	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");;