metadata: run_metadata: 661 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "unspecified" and experiment.platform = "ILLUMINA"

661 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "unspecified" and experiment.platform = "ILLUMINA"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.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
10056	10056	ERR4691987	ERX4613068	ERS5216074	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457891	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457891\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 2\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 2\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4	unspecified	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_2.fastq.gz	fastq	1291626898.0	35072619.0	ena RUN UCLA 16 10 2020 22:30:43:819 4	0:36.83 1:0	A:364596432;C:305716590;G:295397140;T:324498501;N:1418235	36	0	364596432	305716590	295397140	324498501	1418235	ERX4613068	ERS5216074	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.93311	0.08182	0.75852	0.54813	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10057	10057	ERR4691986	ERX4613067	ERS5216073	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457890	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457890\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 1\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 1\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3	unspecified	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_1.fastq.gz	fastq	1236033124.0	33559740.0	ena RUN UCLA 16 10 2020 22:30:43:819 3	0:36.83 1:0	A:348518065;C:293502111;G:279181983;T:313506799;N:1324166	36	0	348518065	293502111	279181983	313506799	1324166	ERX4613067	ERS5216073	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92798	0.07907	0.7697	0.5488	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10058	10058	ERR4691985	ERX4613066	ERS5216072	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457889	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457889\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 2\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 2\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2	unspecified	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_2.fastq.gz	fastq	1180831209.0	32069533.0	ena RUN UCLA 16 10 2020 22:30:43:819 2	0:36.82 1:0	A:328604642;C:281065336;G:278743466;T:291039015;N:1378750	36	0	328604642	281065336	278743466	291039015	1378750	ERX4613066	ERS5216072	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92319	0.08946	0.75706	0.49996	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10059	10059	ERR4691984	ERX4613065	ERS5216071	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457888	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457888\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 1\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 1\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1	unspecified	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_1.fastq.gz	fastq	1428414407.0	38793098.0	ena RUN UCLA 16 10 2020 22:30:43:819 1	0:36.82 1:0	A:398925739;C:338731211;G:333527196;T:355553981;N:1676280	36	0	398925739	338731211	333527196	355553981	1676280	ERX4613065	ERS5216071	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92407	0.08758	0.75726	0.4969	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
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
36761	36761	SRR10295266	SRX7008094	SRS431105	SRP023492	PRJNA206070	Nanog SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition	GSE47558	Other	Upon fertilization maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT a universal step in animal development unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish ZGA is required for gastrulation and clearance of maternal mRNAs which is achieved in part by the conserved microRNA miR 430. However the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation and a failure to activate >75% of zygotic genes. Furthermore we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre and post MZT; ribosome profiling pre MZT		pubmed:24056933		WT 2hpf Total mRNA	GSM1152440		source name:WT 2hpf Total mRNA\|tissue:Whole embryos\|strain:TUAB\|Stage:2hpf\|treatment:n1\|rna subtype:total RNA	WT 64c R0	AGR000324	AGR000324	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP023492			AGR000324_R1.fastq.gz	fastq	781504124.0	10282949.0	AGR000324 R1.fastq.gz	0:76	A:151879560;C:240178928;G:220957551;T:168456166;N:31919	76		151879560	240178928	220957551	168456166	31919	SRX7008094	SRS431105	SRA980383	Yale_Giraldez\|Genetics	Giraldez Lab, Genetics, Yale University	1	0.88875	0.14141	0.796	0.72154	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2019-10-16	Cleavage	Embryo	Whole Organism	All anatomical structures
37921	37921	SRR1554495	SRX685396	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_3.fq.gz	fastq	1225610154.0	12134754.0	Ovary2 Run3	0:101	A:347141358;C:303255805;G:280185540;T:294456010;N:571441	101		347141358	303255805	280185540	294456010	571441	SRX685396	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	1e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37922	37922	SRR1554492	SRX685395	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_3.fq.gz	fastq	1192024422.0	11802222.0	Testis2 Run3	0:101	A:373380865;C:276125943;G:251033102;T:290931637;N:552875	101		373380865	276125943	251033102	290931637	552875	SRX685395	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	1e-05	0.99997	0.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37923	37923	SRR1554489	SRX685394	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_3.fq.gz	fastq	1302765670.0	12898670.0	Heart2 Run3	0:101	A:397689061;C:312745449;G:268626802;T:323141419;N:562939	101		397689061	312745449	268626802	323141419	562939	SRX685394	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	2e-05	0.99997	1.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37924	37924	SRR1554486	SRX685392	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_3.fq.gz	fastq	1211892536.0	11998936.0	Brain2 Run3	0:101	A:374228993;C:286134640;G:253944548;T:297038575;N:545780	101		374228993	286134640	253944548	297038575	545780	SRX685392	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37925	37925	SRR1554483	SRX685391	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_3.fq.gz	fastq	347516154.0	3440754.0	Ovary1 Run3	0:101	A:107805981;C:80183725;G:73617313;T:85763181;N:145954	101		107805981	80183725	73617313	85763181	145954	SRX685391	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05	4e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37926	37926	SRR1554480	SRX685390	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_3.fq.gz	fastq	1184228636.0	11725036.0	Testis1 Run3	0:101	A:340636900;C:278505979;G:259975802;T:304564724;N:545231	101		340636900	278505979	259975802	304564724	545231	SRX685390	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	1e-05	0.0	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37927	37927	SRR1554477	SRX685389	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_3.fq.gz	fastq	1561371524.0	15459124.0	Heart1 Run3	0:101	A:454757966;C:391143691;G:334715236;T:380114024;N:640607	101		454757966	391143691	334715236	380114024	640607	SRX685389	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	2e-05	0.99997	1.0	101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37928	37928	SRR1554474	SRX685388	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_3.fq.gz	fastq	1192445794.0	11806394.0	Brain1 Run3	0:101	A:369786121;C:268557682;G:265557417;T:288006805;N:537769	101		369786121	268557682	265557417	288006805	537769	SRX685388	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	1e-05	1.0		101	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37929	37929	SRR1554493	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_1.fq.gz	fastq	476104278.0	9335378.0	Ovary2 Run1	0:51	A:111060704;C:120863975;G:129849761;T:114224677;N:105161	51		111060704	120863975	129849761	114224677	105161	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00027	8e-05	0.99945	0.8125	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37930	37930	SRR1554494	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_2.fq.gz	fastq	561956352.0	11018752.0	Ovary2 Run2	0:51	A:129925815;C:148479658;G:148478706;T:132824290;N:2247883	51		129925815	148479658	148478706	132824290	2247883	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022	0.0001	0.99967	0.6875	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37931	37931	SRR1554490	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_1.fq.gz	fastq	586152231.0	11493181.0	Testis2 Run1	0:51	A:145360493;C:148943988;G:151402108;T:140286245;N:159397	51		145360493	148943988	151402108	140286245	159397	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05	2e-05	0.99985	0.57142	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37932	37932	SRR1554491	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_2.fq.gz	fastq	697016337.0	13666987.0	Testis2 Run2	0:51	A:172082858;C:184634425;G:173370430;T:163527914;N:3400710	51		172082858	184634425	173370430	163527914	3400710	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05	2e-05	0.99985	0.57142	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37933	37933	SRR1554487	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_1.fq.gz	fastq	767836212.0	15055612.0	Heart2 Run1	0:51	A:192620363;C:202013249;G:191038597;T:181862075;N:301928	51		192620363	202013249	191038597	181862075	301928	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05	3e-05	0.99995	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37934	37934	SRR1554488	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_2.fq.gz	fastq	979886205.0	19213455.0	Heart2 Run2	0:51	A:246169086;C:264387065;G:236377487;T:227289693;N:5662874	51		246169086	264387065	236377487	227289693	5662874	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37935	37935	SRR1554484	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_1.fq.gz	fastq	654412671.0	12831621.0	Brain2 Run1	0:51	A:160544180;C:166355290;G:168608762;T:158684308;N:220131	51		160544180	166355290	168608762	158684308	220131	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05	0.0	0.99993	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37936	37936	SRR1554485	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_2.fq.gz	fastq	856322793.0	16790643.0	Brain2 Run2	0:51	A:210706815;C:226772546;G:212404752;T:201722093;N:4716587	51		210706815	226772546	212404752	201722093	4716587	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37937	37937	SRR1554481	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_1.fq.gz	fastq	116086965.0	2276215.0	Ovary1 Run1	0:51	A:29237121;C:30235277;G:29264328;T:27320814;N:29425	51		29237121	30235277	29264328	27320814	29425	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022	9e-05	0.99967	0.65	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37938	37938	SRR1554482	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_2.fq.gz	fastq	138905844.0	2723644.0	Ovary1 Run2	0:51	A:34695180;C:38015933;G:33434207;T:32057083;N:703441	51		34695180	38015933	33434207	32057083	703441	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00016	5e-05	0.99977	0.42857	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37939	37939	SRR1554478	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_1.fq.gz	fastq	655515750.0	12853250.0	Testis1 Run1	0:51	A:152422885;C:163771947;G:179144090;T:159997538;N:179290	51		152422885	163771947	179144090	159997538	179290	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0011	0.00053	0.99829	0.67777	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37940	37940	SRR1554479	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_2.fq.gz	fastq	777594399.0	15246949.0	Testis1 Run2	0:51	A:180116528;C:202508153;G:204833105;T:186435696;N:3700917	51		180116528	202508153	204833105	186435696	3700917	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00073	0.00032	0.99898	0.62745	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37941	37941	SRR1554475	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_1.fq.gz	fastq	810162642.0	15885542.0	Heart1 Run1	0:51	A:199665102;C:213941735;G:204361738;T:191870055;N:324012	51		199665102	213941735	204361738	191870055	324012	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	6e-05	1e-05	0.99989	0.8	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37942	37942	SRR1554476	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_2.fq.gz	fastq	1013563698.0	19873798.0	Heart1 Run2	0:51	A:249913434;C:275453651;G:247166233;T:235034199;N:5996181	51		249913434	275453651	247166233	235034199	5996181	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	4e-05	2e-05	0.99997	0.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37943	37943	SRR1554472	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_1.fq.gz	fastq	679860294.0	13330594.0	Brain1 Run1	0:51	A:167202435;C:176450132;G:174468721;T:161497185;N:241821	51		167202435	176450132	174468721	161497185	241821	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37944	37944	SRR1554473	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.	miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_2.fq.gz	fastq	838372782.0	16438682.0	Brain1 Run2	0:51	A:206906228;C:221202670;G:210716690;T:195319694;N:4227500	51		206906228	221202670	210716690	195319694	4227500	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
39687	39687	SRR2051113	SRX1048368	SRS952733	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P39		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 4	P39	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4090297192.0	40497992.0	P39	0:101	A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421	101		1016157993	993771683	965986507	1113686588	694421	SRX1048368	SRS952733	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9417	0.14428	0.68937	0.5438	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39688	39688	SRR2051110	SRX1048367	SRS952731	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P37		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 3	P37	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4647442886.0	46014286.0	P37	0:101	A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479	101		1149955739	1129088798	1093234722	1274375148	788479	SRX1048367	SRS952731	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94585	0.12571	0.68633	0.52597	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39689	39689	SRR2051112	SRX1048366	SRS952732	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P36		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 2	P36	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4296894611.0	42543511.0	P36	0:101	A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407	101		1050039699	1061123166	1022913715	1162094624	723407	SRX1048366	SRS952732	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94977	0.13188	0.70976	0.52728	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39690	39690	SRR2051109	SRX1048365	SRS952730	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P35		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 1	P35	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4094752706.0	40542106.0	P35	0:101	A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167	101		1009779802	1004374749	969241794	1110655194	701167	SRX1048365	SRS952730	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94442	0.13203	0.70023	0.53953	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39691	39691	SRR2051102	SRX1048364	SRS952729	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P29		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 4	P29	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4983571896.0	49342296.0	P29	0:101	A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841	101		1247122516	1202173111	1173654831	1359775597	845841	SRX1048364	SRS952729	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94329	0.13234	0.68286	0.51586	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39692	39692	SRR2051100	SRX1048363	SRS952727	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P28		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 3	P28	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4032678914.0	39927514.0	P28	0:101	A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488	101		1015356577	970369004	937306142	1108957703	689488	SRX1048363	SRS952727	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.93887	0.13869	0.69079	0.52237	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39693	39693	SRR2051101	SRX1048362	SRS952728	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P26		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 2	P26	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz	fastq fastq fastq fastq	6526758875.0	64621375.0	P26	0:101	A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228	101		1635664768	1568967965	1518148006	1802863908	1114228	SRX1048362	SRS952728	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.93822	0.15203	0.68609	0.53171	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39694	39694	SRR2051096	SRX1048361	SRS952726	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P25		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 1	P25	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4185957322.0	41445122.0	P25	0:101	A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428	101		1081936223	978799105	956795307	1167714259	712428	SRX1048361	SRS952726	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9288	0.17032	0.6801	0.51298	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39695	39695	SRR2051095	SRX1048360	SRS952725	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P19		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 4	P19	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4293546461.0	42510361.0	P19	0:101	A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822	101		1062707728	1045602693	1011860446	1172670772	704822	SRX1048360	SRS952725	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94381	0.13697	0.69051	0.51415	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39696	39696	SRR2051094	SRX1048359	SRS952724	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P18		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 3	P18	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4257944163.0	42157863.0	P18	0:101	A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125	101		1044532409	1049992329	1010166097	1152524203	729125	SRX1048359	SRS952724	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94262	0.14592	0.69014	0.52498	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39697	39697	SRR2051093	SRX1048358	SRS952723	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P17		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 2	P17	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4278385553.0	42360253.0	P17	0:101	A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139	101		1040955882	1060023973	1019487833	1157186726	731139	SRX1048358	SRS952723	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94697	0.14458	0.69643	0.53451	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39698	39698	SRR2051092	SRX1048357	SRS952722	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P15		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 1	P15	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4341747499.0	42987599.0	P15	0:101	A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377	101		1052621077	1088380866	1041958433	1158051746	735377	SRX1048357	SRS952722	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94563	0.153	0.69822	0.54133	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39699	39699	SRR2051091	SRX1048356	SRS952721	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN9		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 4	CN9	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4220387212.0	41786012.0	CN9	0:101	A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235	101		1031722430	1044497851	1005706674	1137783022	677235	SRX1048356	SRS952721	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.95231	0.14084	0.69682	0.52966	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39700	39700	SRR2051090	SRX1048354	SRS952719	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN8		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 3	CN8	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz	fastq fastq fastq fastq	5835502553.0	57777253.0	CN8	0:101	A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739	101		1424369529	1441755207	1391851806	1576540272	985739	SRX1048354	SRS952719	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94643	0.12925	0.70725	0.52949	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39701	39701	SRR2050894	SRX1048353	SRS952718	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN7		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 2	CN7	1	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4789094477.0	47416777.0	CN7	0:101	A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016	101		1160528098	1197558725	1155573375	1274638263	796016	SRX1048353	SRS952718	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9501	0.14828	0.69966	0.52764	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39702	39702	SRR2050892	SRX1048352	SRS952717	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN5		breed:wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 1	CN5	CN5 EL4506 TGACCA	1	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4526144512.0	44813312.0	CN5	0:101	A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159	101		1109966549	1116619353	1075422479	1223366972	769159	SRX1048352	SRS952717	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94604	0.14084	0.69004	0.53407	101	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
41827	41827	SRR5251446	SRX2557171	SRS1974564	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR139 B1	nicoli mutmir AG01645		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B1	AG01645.1	AG01645.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01645.1_R1.fastq.gz	fastq	1574284140.0	20714265.0	AG01645.1 R1.fastq.gz	0:76	A:485471345;C:270854124;G:374164721;T:443766613;N:27337	76		485471345	270854124	374164721	443766613	27337	SRX2557171	SRS1974564	SRA537606	Yale University\|Genetics	Yale University	1	0.82142	0.14068	0.8002	0.5444	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-27	Undetermined	Embryo	Endothelium	Cardiovascular System
41828	41828	SRR5251445	SRX2557170	SRS1974563	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR139 B2	nicoli mutmir AG01646		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B2	AG01646.1	AG01646.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01646.1_R1.fastq.gz	fastq	1484740104.0	19536054.0	AG01646.1 R1.fastq.gz	0:76	A:453388316;C:246477203;G:365031959;T:419816346;N:26280	76		453388316	246477203	365031959	419816346	26280	SRX2557170	SRS1974563	SRA537606	Yale University\|Genetics	Yale University	1	0.82649	0.1897	0.79862	0.52759	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41829	41829	SRR5251444	SRX2557169	SRS1974562	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR139 B3	nicoli mutmir AG01647		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR139 B3	AG01647.1	AG01647.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01647.1_R1.fastq.gz	fastq	881298660.0	11596035.0	AG01647.1 R1.fastq.gz	0:76	A:270675838;C:160127586;G:228157662;T:222301246;N:36328	76		270675838	160127586	228157662	222301246	36328	SRX2557169	SRS1974562	SRA537606	Yale University\|Genetics	Yale University	1	0.76133	0.15034	0.83341	0.56596	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41830	41830	SRR5251443	SRX2557168	SRS1974561	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR139 B1	nicoli mutmir AG01648		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B1	AG01648.1	AG01648.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01648.1_R1.fastq.gz	fastq	637896880.0	8393380.0	AG01648.1 R1.fastq.gz	0:76	A:192829278;C:112701153;G:153321271;T:179019095;N:26083	76		192829278	112701153	153321271	179019095	26083	SRX2557168	SRS1974561	SRA537606	Yale University\|Genetics	Yale University	1	0.75971	0.1181	0.82171	0.56797	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41831	41831	SRR5251442	SRX2557167	SRS1974560	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR139 B2	nicoli mutmir AG01649		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B2	AG01649.1	AG01649.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01649.1_R1.fastq.gz	fastq	849868328.0	11182478.0	AG01649.1 R1.fastq.gz	0:76	A:258225905;C:148467172;G:205165181;T:237974100;N:35970	76		258225905	148467172	205165181	237974100	35970	SRX2557167	SRS1974560	SRA537606	Yale University\|Genetics	Yale University	1	0.75096	0.14506	0.81507	0.5545	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41832	41832	SRR5251441	SRX2557166	SRS1974559	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR139 B3	nicoli mutmir AG01650		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR139 B3	AG01650.1	AG01650.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01650.1_R1.fastq.gz	fastq	998464668.0	13137693.0	AG01650.1 R1.fastq.gz	0:76	A:311526420;C:176545041;G:251852786;T:258497630;N:42791	76		311526420	176545041	251852786	258497630	42791	SRX2557166	SRS1974559	SRA537606	Yale University\|Genetics	Yale University	1	0.76479	0.11192	0.82674	0.54621	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41833	41833	SRR5251440	SRX2557165	SRS1974558	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR24 B1	nicoli mutmir AG01651		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B1	AG01651.1	AG01651.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01651.1_R1.fastq.gz	fastq	570492252.0	7506477.0	AG01651.1 R1.fastq.gz	0:76	A:162512811;C:104071716;G:135730697;T:168149427;N:27601	76		162512811	104071716	135730697	168149427	27601	SRX2557165	SRS1974558	SRA537606	Yale University\|Genetics	Yale University	1	0.73988	0.10157	0.86647	0.54252	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41834	41834	SRR5251439	SRX2557164	SRS1974557	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR24 B2	nicoli mutmir AG01652		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B2	AG01652.1	AG01652.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01652.1_R1.fastq.gz	fastq	1072886148.0	14116923.0	AG01652.1 R1.fastq.gz	0:76	A:338399596;C:192703439;G:242960887;T:298769761;N:52465	76		338399596	192703439	242960887	298769761	52465	SRX2557164	SRS1974557	SRA537606	Yale University\|Genetics	Yale University	1	0.76456	0.11024	0.89197	0.59214	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41835	41835	SRR5251438	SRX2557163	SRS1974556	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR24 B3	nicoli mutmir AG01653		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR24 B3	AG01653.1	AG01653.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01653.1_R1.fastq.gz	fastq	1016374144.0	13373344.0	AG01653.1 R1.fastq.gz	0:76	A:310958343;C:168702106;G:223420046;T:313241363;N:52286	76		310958343	168702106	223420046	313241363	52286	SRX2557163	SRS1974556	SRA537606	Yale University\|Genetics	Yale University	1	0.75735	0.12224	0.79756	0.55136	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41836	41836	SRR5251437	SRX2557162	SRS1974555	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR24 B1	nicoli mutmir AG01654		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B1	AG01654.1	AG01654.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01654.1_R1.fastq.gz	fastq	782170112.0	10291712.0	AG01654.1 R1.fastq.gz	0:76	A:238316720;C:132163709;G:179301544;T:232350598;N:37541	76		238316720	132163709	179301544	232350598	37541	SRX2557162	SRS1974555	SRA537606	Yale University\|Genetics	Yale University	1	0.7683	0.10712	0.80034	0.55804	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41837	41837	SRR5251436	SRX2557161	SRS1974554	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR24 B2	nicoli mutmir AG01655		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B2	AG01655.1	AG01655.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01655.1_R1.fastq.gz	fastq	1053946340.0	13867715.0	AG01655.1 R1.fastq.gz	0:76	A:318351311;C:191163031;G:240348413;T:304030367;N:53218	76		318351311	191163031	240348413	304030367	53218	SRX2557161	SRS1974554	SRA537606	Yale University\|Genetics	Yale University	1	0.77588	0.07983	0.83934	0.56228	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41838	41838	SRR5251435	SRX2557160	SRS1974553	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR24 B3	nicoli mutmir AG01656		strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR24 B3	AG01656.1	AG01656.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01656.1_R1.fastq.gz	fastq	1182467736.0	15558786.0	AG01656.1 R1.fastq.gz	0:76	A:344465226;C:204677242;G:269228338;T:364036735;N:60195	76		344465226	204677242	269228338	364036735	60195	SRX2557160	SRS1974553	SRA537606	Yale University\|Genetics	Yale University	1	0.78956	0.13495	0.81517	0.56342	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41839	41839	SRR5251434	SRX2557159	SRS1974552	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR223 B1	nicoli mutmir AG01657		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B1	AG01657.1	AG01657.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01657.1_R1.fastq.gz	fastq	536336712.0	7057062.0	AG01657.1 R1.fastq.gz	0:76	A:158301607;C:93070120;G:121382262;T:163555487;N:27236	76		158301607	93070120	121382262	163555487	27236	SRX2557159	SRS1974552	SRA537606	Yale University\|Genetics	Yale University	1	0.76425	0.1278	0.84222	0.55305	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41840	41840	SRR5251433	SRX2557158	SRS1974551	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR223 B2	nicoli mutmir AG01658		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B2	AG01658.1	AG01658.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01658.1_R1.fastq.gz	fastq	798581856.0	10507656.0	AG01658.1 R1.fastq.gz	0:76	A:241352089;C:134327379;G:183394123;T:239469845;N:38420	76		241352089	134327379	183394123	239469845	38420	SRX2557158	SRS1974551	SRA537606	Yale University\|Genetics	Yale University	1	0.76221	0.13398	0.82459	0.55228	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41841	41841	SRR5251432	SRX2557157	SRS1974550	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs WT miR223 B3	nicoli mutmir AG01659		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:3\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs WT miR223 B3	AG01659.1	AG01659.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01659.1_R1.fastq.gz	fastq	1093998948.0	14394723.0	AG01659.1 R1.fastq.gz	0:76	A:330741822;C:186325335;G:249557623;T:327320449;N:53719	76		330741822	186325335	249557623	327320449	53719	SRX2557157	SRS1974550	SRA537606	Yale University\|Genetics	Yale University	1	0.77108	0.14674	0.80955	0.55819	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41842	41842	SRR5251431	SRX2557156	SRS1974549	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR223 B1	nicoli mutmir AG01660		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR223 B1	AG01660.1	AG01660.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01660.1_R1.fastq.gz	fastq	849905492.0	11182967.0	AG01660.1 R1.fastq.gz	0:76	A:250953875;C:146191904;G:190040699;T:262674911;N:44103	76		250953875	146191904	190040699	262674911	44103	SRX2557156	SRS1974549	SRA537606	Yale University\|Genetics	Yale University	1	0.7687	0.14192	0.82842	0.5344	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41843	41843	SRR5251430	SRX2557155	SRS1974548	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.				QuantSeq mutant miRNAs Mut miR223 B2	nicoli mutmir AG01661		strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal	QuantSeq mutant miRNAs Mut miR223 B2	AG01661.1	AG01661.1	1	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP099466			AG01661.1_R1.fastq.gz	fastq	840115400.0	11054150.0	AG01661.1 R1.fastq.gz	0:76	A:257057495;C:141775085;G:188281166;T:252960590;N:41064	76		257057495	141775085	188281166	252960590	41064	SRX2557155	SRS1974548	SRA537606	Yale University\|Genetics	Yale University	1	0.74292	0.10759	0.83615	0.55136	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
43058	43058	SRR8354695	SRX5165478	SRS4174524	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				DMS seq RNA structure positive controls in vitro replicate 1	DMS seq RNA positives ctrl in vitro B1 AG01489		strain:TU/AB\|age:3.7\|dev stage:oblong\|sex:pooled male and female\|tissue:embryo\|treatment:0.5% DMS for 10 min in vitro\|molecule:RNA\|condition:invitro DMS\|replicate group:1\|replicate:1\|barcode:TCTC\|BioSampleModel:Model organism or animal	DMS seq RNA structure positive controls in vitro replicate 1	AG01489.1	AG01489.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			AG01489.1_R1.fastq.gz	fastq	75703530.0	2718404.0	AG01489.1 R1.fastq.gz	0:27.85 1:0	A:18206335;C:19464567;G:21319876;T:16712584;N:168	27	0	18206335	19464567	21319876	16712584	168	SRX5165478	SRS4174524	SRA825010	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.02389	0.00591	0.97654	0.4758	25	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-12-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
43059	43059	SRR8354696	SRX5165477	SRS4174523	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				DMS seq RNA structure positive controls in vitro replicate 2	DMS seq RNA positives ctrl in vitro B2 AG01490		strain:TU/AB\|age:3.7\|dev stage:oblong\|sex:pooled male and female\|tissue:embryo\|treatment:0.5% DMS for 10 min in vitro\|molecule:RNA\|condition:invitro DMS\|replicate group:1\|replicate:2\|barcode:GTGT\|BioSampleModel:Model organism or animal	DMS seq RNA structure positive controls in vitro replicate 2	AG01490.1	AG01490.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			AG01490.1_R1.fastq.gz	fastq	295051199.0	10869746.0	AG01490.1 R1.fastq.gz	0:27.14 1:0	A:71900468;C:76519029;G:81589099;T:65042019;N:584	27	0	71900468	76519029	81589099	65042019	584	SRX5165477	SRS4174523	SRA825010	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.02362	0.00528	0.98173	0.35096	19	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-12-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
43060	43060	SRR8354697	SRX5165476	SRS4174522	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 RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2	Raw multiplex: DMS seq RNA positives ctrl in vitro B1 AG01489;DMS seq RNA positives ctrl in vitro B2 AG01490		strain:TU/AB\|age:3.7\|dev stage:oblong\|sex:pooled male and female\|tissue:embryo\|treatment:0.5% DMS for 10 min in vitro\|molecule:RNA\|condition:invitro DMS\|replicate group:1\|replicate:1;2\|barcode:TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: DMS seq RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2	AG01489.1;AG01490.1	AG01489.1;AG01490.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MYYANXX_JBDX127_009_R1.fastq.gz	fastq	1115150128.0	14673028.0	C7MYYANXX JBDX127 009 R1.fastq.gz	0:76	A:313482382;C:276309346;G:291633361;T:233659719;N:65320	76		313482382	276309346	291633361	233659719	65320	SRX5165476	SRS4174522	SRA825010	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00546	0.00047	0.98602	0.51535	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-12-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
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
43071	43071	SRR7264575	SRX4168722	SRS3380686	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 CHX B1;DMS Seq WT 64c CHX B2	Raw multiplex: dmsseq AG01273;dmsseq AG01274		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo cyclohex\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:18\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2	AG01273.4;AG01274.4	AG01273.4;AG01274.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HWKVWADXX_JBCZ103_023_R1.fastq.gz	fastq	7514617040.0	98876540.0	HWKVWADXX JBCZ103 023 R1.fastq.gz	0:76	A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367	76		2401597632	1861527917	1834777254	1415956870	757367	SRX4168722	SRS3380686	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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43072	43072	SRR7264576	SRX4168721	SRS3380689	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: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2	Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:cyclohex\|molecule:RNA\|condition:RPF 28nt\|replicate group:19\|replicate:1;2\|barcode:CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2	AG01409.1;AG01410.1	AG01409.1;AG01410.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MPPANXX_JBDL115_014_R1.fastq.gz	fastq	4944760108.0	65062633.0	C7MPPANXX JBDL115 014 R1.fastq.gz	0:76	A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198	76		1280812305	1385761238	1441128504	836702863	355198	SRX4168721	SRS3380689	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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43073	43073	SRR7264577	SRX4168720	SRS3380688	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: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2	Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:cyclohex PatA\|molecule:RNA\|condition:RPF 28nt\|replicate group:20\|replicate:1;2\|barcode:CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2	AG01411.1;AG01412.1	AG01411.1;AG01412.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MPPANXX_JBDM116_015_R1.fastq.gz	fastq	10995071544.0	144671994.0	C7MPPANXX JBDM116 015 R1.fastq.gz	0:76	A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089	76		2850888928	3075001734	3215965099	1852417694	798089	SRX4168720	SRS3380688	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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43074	43074	SRR7264578	SRX4168719	SRS3380687	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 PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:21\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	AG01426.1;AG01427.1	AG01426.1;AG01427.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MPPANXX_JBDF109_027_R1.fastq.gz	fastq	446991948.0	5881473.0	C7MPPANXX JBDF109 027 R1.fastq.gz	0:76	A:146192524;C:109441919;G:103882304;T:87445288;N:29913	76		146192524	109441919	103882304	87445288	29913	SRX4168719	SRS3380687	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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43075	43075	SRR7264579	SRX4168718	SRS3380687	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 PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:21\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	AG01426.2;AG01427.2	AG01426.2;AG01427.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJC2ADXX_JBDF109_027_R1.fastq.gz	fastq	447485492.0	5887967.0	HVJC2ADXX JBDF109 027 R1.fastq.gz	0:76	A:146683880;C:109166579;G:104154702;T:87473352;N:6979	76		146683880	109166579	104154702	87473352	6979	SRX4168718	SRS3380687	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0023	0.00034	0.99326	0.57567	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43076	43076	SRR7264580	SRX4168717	SRS3380687	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 PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:21\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	AG01426.3;AG01427.3	AG01426.3;AG01427.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJ2TADXX_JBDF109_027_R1.fastq.gz	fastq	4740289176.0	62372226.0	HVJ2TADXX JBDF109 027 R1.fastq.gz	0:76	A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336	76		1552060471	1156267615	1104246757	927209997	504336	SRX4168717	SRS3380687	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00235	0.00026	0.99379	0.60051	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43077	43077	SRR7264581	SRX4168716	SRS3380687	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 PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:21\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2	AG01426.4;AG01427.4	AG01426.4;AG01427.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz	fastq	6776423036.0	89163461.0	HJTYNBCXX JBDF109 NOBCX R1.fastq.gz	0:76	A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906	76		2212424663	1653496002	1573846163	1336100302	555906	SRX4168716	SRS3380687	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	3e-05	2e-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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43078	43078	SRR7264582	SRX4168715	SRS3380683	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 PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS PatA\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:22\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	AG01428.1;AG01429.1	AG01428.1;AG01429.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MPPANXX_JBDG110_013_R1.fastq.gz	fastq	1593732388.0	20970163.0	C7MPPANXX JBDG110 013 R1.fastq.gz	0:76	A:517196379;C:393268952;G:372639155;T:310521534;N:106368	76		517196379	393268952	372639155	310521534	106368	SRX4168715	SRS3380683	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	2e-05	0.0	0.99997	1.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43079	43079	SRR7264583	SRX4168714	SRS3380683	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 PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS PatA\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:22\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	AG01428.2;AG01429.2	AG01428.2;AG01429.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJC2ADXX_JBDG110_013_R1.fastq.gz	fastq	1268326988.0	16688513.0	HVJC2ADXX JBDG110 013 R1.fastq.gz	0:76	A:411772190;C:312434121;G:297408612;T:246654231;N:57834	76		411772190	312434121	297408612	246654231	57834	SRX4168714	SRS3380683	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	1e-05	0.0	0.99997	0.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43080	43080	SRR7264584	SRX4168713	SRS3380683	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 PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS PatA\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:22\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	AG01428.3;AG01429.3	AG01428.3;AG01429.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJ2TADXX_JBDG110_013_R1.fastq.gz	fastq	1149592188.0	15126213.0	HVJ2TADXX JBDG110 013 R1.fastq.gz	0:76	A:373090462;C:283151050;G:269811169;T:223419849;N:119658	76		373090462	283151050	269811169	223419849	119658	SRX4168713	SRS3380683	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00222	0.0002	0.99362	0.55643	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43081	43081	SRR7264585	SRX4168712	SRS3380686	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 CHX B1;DMS Seq WT 64c CHX B2	Raw multiplex: dmsseq AG01273;dmsseq AG01274		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo cyclohex\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:18\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2	AG01273.3;AG01274.3	AG01273.3;AG01274.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJ7NADXX_JBCZ103_023_R1.fastq.gz	fastq	882016024.0	11605474.0	HVJ7NADXX JBCZ103 023 R1.fastq.gz	0:76	A:278837606;C:213606139;G:214029888;T:175477675;N:64716	76		278837606	213606139	214029888	175477675	64716	SRX4168712	SRS3380686	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	6e-05	4e-05	0.99995	1.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43082	43082	SRR7264586	SRX4168711	SRS3380686	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 CHX B1;DMS Seq WT 64c CHX B2	Raw multiplex: dmsseq AG01273;dmsseq AG01274		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo cyclohex\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:18\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2	AG01273.2;AG01274.2	AG01273.2;AG01274.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVK53ADXX_JBCZ103_023_R1.fastq.gz	fastq	2614864056.0	34406106.0	HVK53ADXX JBCZ103 023 R1.fastq.gz	0:76	A:832670351;C:647746556;G:639758530;T:494461931;N:226688	76		832670351	647746556	639758530	494461931	226688	SRX4168711	SRS3380686	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	5e-05	2e-05	0.99993	0.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43083	43083	SRR7264587	SRX4168710	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.4;AG01270.4	AG01269.4;AG01270.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MYYANXX_JBCX101_016_R1.fastq.gz	fastq	3504515800.0	46112050.0	C7MYYANXX JBCX101 016 R1.fastq.gz	0:76	A:1100987855;C:897481291;G:850509260;T:655386223;N:151171	76		1100987855	897481291	850509260	655386223	151171	SRX4168710	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00251	0.00024	0.99334	0.49363	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43084	43084	SRR7264588	SRX4168709	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.3;AG01270.3	AG01269.3;AG01270.3	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJ7NADXX_JBCX101_016_R1.fastq.gz	fastq	1533760484.0	20181059.0	HVJ7NADXX JBCX101 016 R1.fastq.gz	0:76	A:486730101;C:387546602;G:372319444;T:287072948;N:91389	76		486730101	387546602	372319444	287072948	91389	SRX4168709	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	4e-05	2e-05	0.99997	1.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43085	43085	SRR7264589	SRX4168708	SRS3380686	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 CHX B1;DMS Seq WT 64c CHX B2	Raw multiplex: dmsseq AG01273;dmsseq AG01274		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS in vivo cyclohex\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:18\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2	AG01273.1;AG01274.1	AG01273.1;AG01274.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HMHGVADXX_JBCZ103_023_R1.fastq.gz	fastq	2819768568.0	37102218.0	HMHGVADXX JBCZ103 023 R1.fastq.gz	0:76	A:900945260;C:699348182;G:689446355;T:529699985;N:328786	76		900945260	699348182	689446355	529699985	328786	SRX4168708	SRS3380686	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	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43086	43086	SRR7264590	SRX4168707	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.5;AG01270.5	AG01269.5;AG01270.5	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MWLANXX_JBCX101_016_R1.fastq.gz	fastq	11187105076.0	147198751.0	C7MWLANXX JBCX101 016 R1.fastq.gz	0:76	A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660	76		3525623658	2869684594	2708534500	2083102664	159660	SRX4168707	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
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
43089	43089	SRR7264593	SRX4168704	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.2;AG01270.2	AG01269.2;AG01270.2	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVK53ADXX_JBCX101_016_R1.fastq.gz	fastq	4318423208.0	56821358.0	HVK53ADXX JBCX101 016 R1.fastq.gz	0:76	A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019	76		1370691469	1101595011	1048719303	796936406	481019	SRX4168704	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	1e-05	0.0	0.99997	0.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43090	43090	SRR7264594	SRX4168703	SRS3380684	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	Raw multiplex: dmsseq AG01269;dmsseq AG01270		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS 0.5% in vitro\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:17\|replicate:2;1\|barcode:AGAG;CACA\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1	AG01269.1;AG01270.1	AG01269.1;AG01270.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HMHGVADXX_JBCX101_016_R1.fastq.gz	fastq	3247405520.0	42729020.0	HMHGVADXX JBCX101 016 R1.fastq.gz	0:76	A:1030573532;C:829398246;G:789085434;T:598013908;N:334400	76		1030573532	829398246	789085434	598013908	334400	SRX4168703	SRS3380684	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
43091	43091	SRR7264595	SRX4168702	SRS3380683	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 PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS PatA\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:22\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	AG01428.5;AG01429.5	AG01428.5;AG01429.5	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HJTYNBCXX_JBDG110_NOBCX_R1.fastq.gz	fastq	8473348224.0	111491424.0	HJTYNBCXX JBDG110 NOBCX R1.fastq.gz	0:76	A:2738474380;C:2086110939;G:1986494866;T:1661471870;N:796169	76		2738474380	2086110939	1986494866	1661471870	796169	SRX4168702	SRS3380683	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	3e-05	2e-05	1.0		76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43092	43092	SRR7264596	SRX4168701	SRS3380683	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 PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429		strain:TU/AB\|age:2\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:DMS PatA\|molecule:RNA\|selection:pA\|condition:DMS\|replicate group:22\|replicate:1;2\|barcode:CACA;AGAG\|BioSampleModel:Model organism or animal	Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2	AG01428.4;AG01429.4	AG01428.4;AG01429.4	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			HVJ7NADXX_JBDG110_013_R1.fastq.gz	fastq	1317100672.0	17330272.0	HVJ7NADXX JBDG110 013 R1.fastq.gz	0:76	A:424319849;C:318879376;G:308835829;T:264971153;N:94465	76		424319849	318879376	308835829	264971153	94465	SRX4168701	SRS3380683	SRA715414	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	9e-05	5e-05	0.99995	0.2	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-05	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
43093	43093	SRR5893052	SRX3058793	SRS2404523	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				miniRESA 6h a Am pA RNA B1	miniresa AG01714		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:27\|replicate:1\|BioSampleModel:Model organism or animal	miniRESA 6h a Am pA RNA B1	AG01714.1	AG01714.1	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			AG01714.1_R1.fastq.gz	fastq	263900576.0	3472376.0	AG01714.1 R1.fastq.gz	0:76	A:71973779;C:48927629;G:51913512;T:91079622;N:6034	76		71973779	48927629	51913512	91079622	6034	SRX3058793	SRS2404523	SRA596275	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.9163	3e-05	0.99833	0.61085	76	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2018-06-07	Gastrula	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");;