metadata: run_metadata: 20 rows where devstage_curation = "Multi-stage" and experiment.library

20 rows where devstage_curation = "Multi-stage" and experiment.library_selection = "unspecified"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10213	10213	ERR6511329	ERX6138165	ERS7264188	ERP131213	PRJEB46978	Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing	ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159	Other	Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome.	ENA FIRST PUBLIC:2023 12 28\|ENA LAST UPDATE:2023 12 28	Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs	Zebrafish Ribodep Rep1	SAMEA9541418	CENTER FOR GENOMIC REGULATION (CRG)	ENA FIRST PUBLIC:2023 12 28T01:07:23Z\|ENA LAST UPDATE:2023 12 28T01:07:23Z\|External Id:SAMEA9541418\|INSDC center name:CENTER FOR GENOMIC REGULATION CRG\|INSDC first public:2023 12 28T01:07:23Z\|INSDC last update:2023 12 28T01:07:23Z\|INSDC status:public\|Submitter Id:Zebrafish Ribodep Rep1\|common name:zebrafish\|sample name:Zebrafish Ribodep Rep1\|scientific name:Danio rerio	MinION sequencing	ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3	cDNA786327	Nano3P seq	Nano3P seq	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	OXFORD_NANOPORE	MinION	ERP131213	MinION sequencing	ENA FIRST PUBLIC:2023 12 28\|ENA LAST UPDATE:2023 12 28	zebrafish_ribodep_rep1.tar.gz	nanopore	1745399583.0	1644167.0	ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3	0:1061.57	A:449704009;C:421915878;G:378879857;T:494899839;N:0	1061		449704009	421915878	378879857	494899839	0	ERX6138165	ERS7264188	ERA5757997	CENTER FOR GENOMIC REGULATION (CRG)\|European Nucleotide Archive	CENTER FOR GENOMIC REGULATION (CRG)	1	0.01112	0.0	0.99997	1.0	546	T	long read	ont	ont	full_length	rrna_depletion	unknown	bulk	unknown	unknown	Spain	2023-12-28	Multi-stage	Embryo	Undetermined	Embryo Imprecise
10215	10215	ERR6511330	ERX6138166	ERS7264189	ERP131213	PRJEB46978	Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing	ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159	Other	Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome.	ENA FIRST PUBLIC:2023 12 28\|ENA LAST UPDATE:2023 12 28	Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs	Zebrafish Ribodep Rep2	SAMEA9541419	CENTER FOR GENOMIC REGULATION (CRG)	ENA FIRST PUBLIC:2023 12 28T01:07:23Z\|ENA LAST UPDATE:2023 12 28T01:07:23Z\|External Id:SAMEA9541419\|INSDC center name:CENTER FOR GENOMIC REGULATION CRG\|INSDC first public:2023 12 28T01:07:23Z\|INSDC last update:2023 12 28T01:07:23Z\|INSDC status:public\|Submitter Id:Zebrafish Ribodep Rep2\|common name:zebrafish\|sample name:Zebrafish Ribodep Rep2\|scientific name:Danio rerio	MinION sequencing	ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4	cDNA123791	Nano3P seq	Nano3P seq	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	OXFORD_NANOPORE	MinION	ERP131213	MinION sequencing	ENA FIRST PUBLIC:2023 12 28\|ENA LAST UPDATE:2023 12 28	zebrafish_ribodep_rep2.tar.gz	nanopore	2038398139.0	1955617.0	ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4	0:1042.33	A:518369802;C:477535545;G:441294056;T:601198736;N:0	1042		518369802	477535545	441294056	601198736	0	ERX6138166	ERS7264189	ERA5757997	CENTER FOR GENOMIC REGULATION (CRG)\|European Nucleotide Archive	CENTER FOR GENOMIC REGULATION (CRG)									ont	ont	full_length	rrna_depletion	unknown	bulk	unknown	unknown	Spain	2023-12-28	Multi-stage	Embryo	Undetermined	Embryo Imprecise
43061	43061	SRR7264565	SRX4168732	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.2;AG01047.2;AG01049.2;unrelated	AG01046.2;AG01047.2;AG01049.2;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA22NADXX_JBBS71_021_R1.fastq.gz	fastq	493969676.0	6499601.0	HA22NADXX JBBS71 021 R1.fastq.gz	0:76	A:149523181;C:122615352;G:117180131;T:97949905;N:6701107	76		149523181	122615352	117180131	97949905	6701107	SRX4168732	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43062	43062	SRR7264566	SRX4168731	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.1;AG01047.1;AG01049.1;unrelated	AG01046.1;AG01047.1;AG01049.1;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA1YWADXX_JBBS71_021_R1.fastq.gz	fastq	1444702012.0	19009237.0	HA1YWADXX JBBS71 021 R1.fastq.gz	0:76	A:442549747;C:365473385;G:344546726;T:292070542;N:61612	76		442549747	365473385	344546726	292070542	61612	SRX4168731	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43063	43063	SRR7264567	SRX4168730	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.6;AG01043.6;AG01044.6;unrelated	AG01042.6;AG01043.6;AG01044.6;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HBCAFADXX_JBBR70_020_R1.fastq.gz	fastq	3562176468.0	46870743.0	HBCAFADXX JBBR70 020 R1.fastq.gz	0:76	A:1097921080;C:906895047;G:849908073;T:707369464;N:82804	76		1097921080	906895047	849908073	707369464	82804	SRX4168730	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43064	43064	SRR7264568	SRX4168729	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.5;AG01043.5;AG01044.5;unrelated	AG01042.5;AG01043.5;AG01044.5;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			C562AACXX_JBBR70_NOBCX_R1.fastq.gz	fastq	13352386192.0	175689292.0	C562AACXX JBBR70 NOBCX R1.fastq.gz	0:76	A:4126007145;C:3372127203;G:3172182791;T:2661287884;N:20781169	76		4126007145	3372127203	3172182791	2661287884	20781169	SRX4168729	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43065	43065	SRR7264569	SRX4168728	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.4;AG01043.4;AG01044.4;unrelated	AG01042.4;AG01043.4;AG01044.4;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA2H1ADXX_JBBR70_NOBCX_R1.fastq.gz	fastq	9139389880.0	120255130.0	HA2H1ADXX JBBR70 NOBCX R1.fastq.gz	0:76	A:2815354570;C:2322972018;G:2180978488;T:1817457488;N:2627316	76		2815354570	2322972018	2180978488	1817457488	2627316	SRX4168728	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43066	43066	SRR7264570	SRX4168727	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.3;AG01043.3;AG01044.3;unrelated	AG01042.3;AG01043.3;AG01044.3;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA1YVADXX_JBBR70_NOBCX_R1.fastq.gz	fastq	7892000132.0	103842107.0	HA1YVADXX JBBR70 NOBCX R1.fastq.gz	0:76	A:2428266964;C:2007082407;G:1885147455;T:1568726692;N:2776614	76		2428266964	2007082407	1885147455	1568726692	2776614	SRX4168727	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43067	43067	SRR7264571	SRX4168726	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.2;AG01043.2;AG01044.2;unrelated	AG01042.2;AG01043.2;AG01044.2;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA22NADXX_JBBR70_020_R1.fastq.gz	fastq	554569568.0	7296968.0	HA22NADXX JBBR70 020 R1.fastq.gz	0:76	A:168630291;C:138451887;G:131779810;T:108186590;N:7520990	76		168630291	138451887	131779810	108186590	7520990	SRX4168726	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43068	43068	SRR7264572	SRX4168725	SRS3380690	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated		strain:TU/AB\|age:2.0;4.0;6.0\|dev stage:64c;sphere;shield\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;15;16\|replicate:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated	AG01042.1;AG01043.1;AG01044.1;unrelated	AG01042.1;AG01043.1;AG01044.1;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA1YWADXX_JBBR70_020_R1.fastq.gz	fastq	1565371316.0	20596991.0	HA1YWADXX JBBR70 020 R1.fastq.gz	0:76	A:481887814;C:398331513;G:374271346;T:310815367;N:65276	76		481887814	398331513	374271346	310815367	65276	SRX4168725	SRS3380690	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43069	43069	SRR7264573	SRX4168724	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.4;AG01047.4;AG01049.4;unrelated	AG01046.4;AG01047.4;AG01049.4;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA2H1ADXX_JBBS71_NOBCX_R1.fastq.gz	fastq	8845878184.0	116393134.0	HA2H1ADXX JBBS71 NOBCX R1.fastq.gz	0:76	A:2711637569;C:2235324807;G:2105535243;T:1791610098;N:1770467	76		2711637569	2235324807	2105535243	1791610098	1770467	SRX4168724	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43070	43070	SRR7264574	SRX4168723	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.3;AG01047.3;AG01049.3;unrelated	AG01046.3;AG01047.3;AG01049.3;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HA1YVADXX_JBBS71_NOBCX_R1.fastq.gz	fastq	7768733452.0	102220177.0	HA1YVADXX JBBS71 NOBCX R1.fastq.gz	0:76	A:2378019627;C:1963788516;G:1851111018;T:1572409542;N:3404749	76		2378019627	1963788516	1851111018	1572409542	3404749	SRX4168723	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	1e-05	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43087	43087	SRR7264591	SRX4168706	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.6;AG01047.6;AG01049.6;unrelated	AG01046.6;AG01047.6;AG01049.6;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			HBCAFADXX_JBBS71_021_R1.fastq.gz	fastq	5103002976.0	67144776.0	HBCAFADXX JBBS71 021 R1.fastq.gz	0:76	A:1565087315;C:1292145008;G:1214936605;T:1030712352;N:121696	76		1565087315	1292145008	1214936605	1030712352	121696	SRX4168706	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	2e-05	1e-05	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
43088	43088	SRR7264592	SRX4168705	SRS3380685	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.			Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated		strain:TU/AB\|age:2.0;6.0;4.0\|dev stage:64c;shield;sphere\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:14;16;15\|replicate:2\|barcode:CACA;TCTC;AGAG;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated	AG01046.5;AG01047.5;AG01049.5;unrelated	AG01046.5;AG01047.5;AG01049.5;unrelated	RNA		OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP114782			C562AACXX_JBBS71_NOBCX_R1.fastq.gz	fastq	11245730944.0	147970144.0	C562AACXX JBBS71 NOBCX R1.fastq.gz	0:76	A:3451642355;C:2826476753;G:2670179644;T:2277897894;N:19534298	76		3451642355	2826476753	2670179644	2277897894	19534298	SRX4168705	SRS3380685	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62513	62513	SRR13234629	SRX9666697	SRS7865633	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf + miR 430 polyA	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24h miR 430 pA AGN000151		strain:TU/AB\|age:24.0\|sex:pooled male and female\|tissue:embryo\|genotype:MZdrosha\|strain maternal:drosha / \|strain paternal:drosha / \|treatment:miR 430\|molecule:RNA\|selection:pA\|sample ref:AGS000139\|replicate ref:AGN000151\|replicate order:1\|BioSampleModel:Model organism or animal	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf + miR 430 polyA	AGR000205	AGR000205	RNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP297464			AGR000205_R1.fastq.gz	fastq	2727788580.0	35891955.0	AGR000205 R1.fastq.gz	0:76 1:0	A:729356309;C:615469895;G:605441208;T:777367849;N:153319	76	0	729356309	615469895	605441208	777367849	153319	SRX9666697	SRS7865633	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.94092	0.11617	0.69812	0.46621	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62514	62514	SRR13234630	SRX9666696	SRS7865634	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf polyA	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24h pA AGN000150		strain:TU/AB\|age:24.0\|sex:pooled male and female\|tissue:embryo\|genotype:MZdrosha\|strain maternal:drosha / \|strain paternal:drosha / \|molecule:RNA\|selection:pA\|sample ref:AGS000138\|replicate ref:AGN000150\|replicate order:1\|BioSampleModel:Model organism or animal	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf polyA	AGR000204	AGR000204	RNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP297464			AGR000204_R1.fastq.gz	fastq	2636487272.0	34690622.0	AGR000204 R1.fastq.gz	0:76 1:0	A:711904145;C:590614495;G:581863191;T:751960867;N:144574	76	0	711904145	590614495	581863191	751960867	144574	SRX9666696	SRS7865634	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.93765	0.12096	0.69187	0.47423	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62515	62515	SRR13234631	SRX9666695	SRS7865632	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf + miR 430 polyA	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24h miR 430 pA AGN000149		strain:TU/AB\|age:24.0\|sex:pooled male and female\|tissue:embryo\|genotype:MZdicer\|strain maternal:dicer / \|strain paternal:dicer / \|treatment:miR 430\|molecule:RNA\|selection:pA\|sample ref:AGS000137\|replicate ref:AGN000149\|replicate order:1\|BioSampleModel:Model organism or animal	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf + miR 430 polyA	AGR000203	AGR000203	RNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP297464			AGR000203_R1.fastq.gz	fastq	2458941240.0	32354490.0	AGR000203 R1.fastq.gz	0:76 1:0	A:658826404;C:554609294;G:545318725;T:700047186;N:139631	76	0	658826404	554609294	545318725	700047186	139631	SRX9666695	SRS7865632	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.93305	0.12726	0.69229	0.47229	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62516	62516	SRR13234632	SRX9666694	SRS7865631	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf polyA	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24h pA AGN000148		strain:TU/AB\|age:24.0\|sex:pooled male and female\|tissue:embryo\|genotype:MZdicer\|strain maternal:dicer / \|strain paternal:dicer / \|molecule:RNA\|selection:pA\|sample ref:AGS000136\|replicate ref:AGN000148\|replicate order:1\|BioSampleModel:Model organism or animal	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf polyA	AGR000202	AGR000202	RNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP297464			AGR000202_R1.fastq.gz	fastq	2774787284.0	36510359.0	AGR000202 R1.fastq.gz	0:76 1:0	A:764934757;C:611096752;G:604464623;T:794135162;N:155990	76	0	764934757	611096752	604464623	794135162	155990	SRX9666694	SRS7865631	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.92824	0.15268	0.70485	0.48175	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62517	62517	SRR13234633	SRX9666693	SRS7865629	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 24hpf polyA	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 WT 24h pA AGN000147		strain:TU/AB\|age:24.0\|sex:pooled male and female\|tissue:embryo\|strain maternal:wild type\|strain paternal:wild type\|molecule:RNA\|selection:pA\|sample ref:AGS000135\|replicate ref:AGN000147\|replicate order:1\|BioSampleModel:Model organism or animal	WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 24hpf polyA	AGR000201	AGR000201	RNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP297464			AGR000201_R1.fastq.gz	fastq	2742017604.0	36079179.0	AGR000201 R1.fastq.gz	0:76 1:0	A:730482205;C:622643706;G:610359881;T:778376331;N:155481	76	0	730482205	622643706	610359881	778376331	155481	SRX9666693	SRS7865629	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.94286	0.103	0.69798	0.47058	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
62539	62539	SRR13234655	SRX9666671	SRS7865608	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.			MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 2hpf polyA	MZythdf2/3 mRNA pA & R0 WT 2h pA AGN002333		strain:TU/AB\|age:2.0\|dev stage:64 cell 128 cell\|sex:pooled male and female\|tissue:embryo\|strain maternal:unrelated TUAB wild type\|strain paternal:unrelated TUAB wild type\|molecule:mRNA\|selection:pA\|sample ref:AGS001762\|replicate ref:AGN002333\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 2hpf polyA	AGR003020	AGR003020	mRNA		RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464			AGR003020_R1.fastq.gz	fastq	585244308.0	7700583.0	AGR003020 R1.fastq.gz	0:76 1:0	A:146436207;C:138168832;G:132640929;T:167963204;N:35136	76	0	146436207	138168832	132640929	167963204	35136	SRX9666671	SRS7865608	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.93873	0.03373	0.76215	0.51712	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-09	Multi-stage	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");;