metadata: run_metadata: 817 rows where experiment.library_selection = "unspecified" and tissue_curation

817 rows where experiment.library_selection = "unspecified" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8055	8055	ERR022484	ERX008924	ERS017427	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				E MTAB 434:ZF 2cells	SAMEA898400	Wellcome Sanger Institute	Alias:E MTAB 434:ZF 2cells\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2011 03 10T17:55:05Z\|INSDC last update:2018 03 08T15:25:14Z\|INSDC status:public\|SRA accession:ERS017427\|Sample Name:ERS017427\|Sex:mixed\|StrainOrLine:Tuebingen\|Title:ZF 2cells	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 2cells	RNA from Zebrafish embryo 2cells	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:cell	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	4946_5.srf	srf	3947547008.0	25970704.0	E MTAB 434:4946 5.srf	0:76 1:76	A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500	76	76	1069302461	914233601	902631356	1055986090	5393500	ERX008924	ERS017427	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.93356	0.93346	0.03988	0.04022	0.79135	0.79198	0.48864	0.48464	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2011-03-10	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
8056	8056	ERR022486	ERX008922	ERS012705	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				E MTAB 308:Zebrafish embryo 1 dpf 2	SAMEA898401	Wellcome Sanger Institute	Age:1 days\|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 08 19T15:57:35Z\|INSDC last update:2018 03 08T15:25:04Z\|INSDC status:public\|InitialTimePoint:fertilization\|OrganismPart:whole organism\|SRA accession:ERS012705\|Sample Name:ERS012705\|Sex:unknown sex\|StrainOrLine:Tuebingen\|Title:Danio rerio	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 1 dpf	RNA from Zebrafish embryo 1 dpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: AGE:1 d\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	5141_3.srf	srf	4788693120.0	31504560.0	E MTAB 434:5141 3.srf	0:76 1:76	A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244	76	76	1329328273	1071568772	1063807333	1316891498	7097244	ERX008922	ERS012705	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.95867	0.95691	0.14543	0.14805	0.69753	0.70078	0.46273	0.47662	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-08-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
8057	8057	ERR022488	ERX008921	ERS012706	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				E MTAB 308:Zebrafish embryo 3 dpf 2	SAMEA898404	Wellcome Sanger Institute	Age:3 days\|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 08 19T15:57:35Z\|INSDC last update:2018 03 08T15:25:04Z\|INSDC status:public\|InitialTimePoint:fertilization\|OrganismPart:whole organism\|SRA accession:ERS012706\|Sample Name:ERS012706\|Sex:unknown sex\|StrainOrLine:Tuebingen\|Title:Danio rerio	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 3 dpf	RNA from Zebrafish embryo 3 dpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: AGE:3 d\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	5141_6.srf	srf	3787933176.0	24920613.0	E MTAB 434:5141 6.srf	0:76 1:76	A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818	76	76	1051092006	842721213	838644314	1048667825	6807818	ERX008921	ERS012706	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.95952	0.95914	0.16277	0.16553	0.66352	0.6661	0.46603	0.46879	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-08-19	Larval	Larval	Whole Organism	All anatomical structures
8058	8058	ERR022485	ERX008920	ERS017423	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				E MTAB 434:ZF 6hpf	SAMEA898399	Wellcome Sanger Institute	Age:6 hours\|Alias:E MTAB 434:ZF 6hpf\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2011 03 10T17:55:05Z\|INSDC last update:2018 03 08T15:25:14Z\|INSDC status:public\|SRA accession:ERS017423\|Sample Name:ERS017423\|Sex:mixed\|StrainOrLine:Tupfel long fin\|Title:ZF 6hpf	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 6hpf	RNA from Zebrafish embryo 6hpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: AGE:6 h\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	4946_6.srf	srf	5910514528.0	38884964.0	E MTAB 434:4946 6.srf	0:76 1:76	A:1741038828;C:1243493514;G:1214904056;T:1703863323;N:7214807	76	76	1741038828	1243493514	1214904056	1703863323	7214807	ERX008920	ERS017423	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.91619	0.91684	0.14961	0.15221	0.77189	0.7723	0.49092	0.49303	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2011-03-10	Gastrula	Embryo	Whole Organism	All anatomical structures
8061	8061	ERR022482	ERX008919	ERS000084	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				5 dpf sample1	SAMEA708828	Wellcome Sanger Institute	Alias:5 dpf sample1\|Description:RNA extracted from zebrafish embryo at 5 dpf\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000084\|Sample Name:ERS000084\|Sex:mixed\|Strain:Tuebingen\|Title:Danio rerio	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 5 dpf	RNA from Zebrafish embryo 5 dpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.	Experimental Factor: AGE:5 d\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	2719_7.srf	srf	1764668160.0	16339520.0	E MTAB 434:2719 7.srf	0:54 1:54	A:470580161;C:399075336;G:417290042;T:474450367;N:3272254	54	54	470580161	399075336	417290042	474450367	3272254	ERX008919	ERS000084	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.9454	0.94288	0.20211	0.2029	0.66856	0.67207	0.4856	0.48119	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Larval	Larval	Whole Organism	All anatomical structures
8062	8062	ERR022483	ERX008919	ERS000084	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				5 dpf sample1	SAMEA708828	Wellcome Sanger Institute	Alias:5 dpf sample1\|Description:RNA extracted from zebrafish embryo at 5 dpf\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000084\|Sample Name:ERS000084\|Sex:mixed\|Strain:Tuebingen\|Title:Danio rerio	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 5 dpf	RNA from Zebrafish embryo 5 dpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.	Experimental Factor: AGE:5 d\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	2719_8.srf	srf	1678321188.0	15540011.0	E MTAB 434:2719 8.srf	0:54 1:54	A:446988405;C:380486018;G:396533911;T:451117596;N:3195258	54	54	446988405	380486018	396533911	451117596	3195258	ERX008919	ERS000084	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.94565	0.94277	0.19929	0.19877	0.66584	0.67014	0.47973	0.46826	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Larval	Larval	Whole Organism	All anatomical structures
8063	8063	ERR022487	ERX008918	ERS012707	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				E MTAB 308:Zebrafish embryo 2 dpf 2	SAMEA898403	Wellcome Sanger Institute	Age:2 days\|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 08 19T15:57:35Z\|INSDC last update:2018 03 08T15:25:04Z\|INSDC status:public\|InitialTimePoint:fertilization\|OrganismPart:whole organism\|SRA accession:ERS012707\|Sample Name:ERS012707\|Sex:unknown sex\|StrainOrLine:Tuebingen\|Title:Danio rerio	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 2 dpf	RNA from Zebrafish embryo 2 dpf	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: AGE:2 d\|Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:whole organism	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	5141_5.srf	srf	4321796696.0	28432873.0	E MTAB 434:5141 5.srf	0:76 1:76	A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424	76	76	1185782721	976784015	973264244	1178952292	7013424	ERX008918	ERS012707	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.96001	0.95851	0.15373	0.15636	0.69051	0.69576	0.47409	0.47525	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-08-19	Hatching	Embryo	Whole Organism	All anatomical structures
36405	36405	SRR546820	SRX180750	SRS347212	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.	pubmed:24531765	Zebrafish wild type AB strain embryo prim6 stage	D. rerio prim6 embryo	D. rerio prim6 embryo			RNAseq D. rerio prim6 embryo	RNAseq D. rerio prim6 embryo	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			RNAseq_prim6_2_fix.fastq	fastq	3011340704.0	19811452.0	RNAseq D. rerio prim6 embryo	0:76 1:76	A:727345664;C:767747833;G:787766862;T:725606403;N:2873942	76	76	727345664	767747833	787766862	725606403	2873942	SRX180750	SRS347212	SRA055273	University of Bergen	ZEPROME consortium	2	0.94491	0.94492	0.04196	0.04323	0.76641	0.76928	0.48087	0.48787	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36406	36406	SRR546819	SRX180749	SRS347211	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.	pubmed:24531765	Zebrafish wild type AB strain embryo 14 somites stage	D. rerio 14 somites embryo	D. rerio 14 somites embryo			RNAseq D. rerio 14 somites embryo	RNAseq D. rerio 14 somites embryo	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			RNAseq_14somites_2.fastq	fastq	2976465520.0	19582010.0	RNAseq D. rerio 14 somites embryo	0:76 1:76	A:747831748;C:733533938;G:754151936;T:738091995;N:2855903	76	76	747831748	733533938	754151936	738091995	2855903	SRX180749	SRS347211	SRA055273	University of Bergen	ZEPROME consortium	2	0.9236	0.91427	0.0861	0.08534	0.7559	0.75528	0.48428	0.47549	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
36407	36407	SRR546818	SRX180748	SRS347209	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.	pubmed:24531765	Zebrafish wild type AB strain embryo dome/zfs:0000015 stage	D. rerio dome/zfs:0000015 embryo	D. rerio dome/zfs:0000015 embryo			RNAseq D. rerio dome/zfs:0000015 embryo	RNAseq D. rerio dome/zfs:0000015 embryo	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			RNAseq_30p_dome_1.fastq	fastq	2359648608.0	15524004.0	RNAseq D. rerio dome/zfs:0000015 embryo	0:76 1:76	A:588562906;C:575605218;G:603310130;T:589755481;N:2414873	76	76	588562906	575605218	603310130	589755481	2414873	SRX180748	SRS347209	SRA055273	University of Bergen	ZEPROME consortium	2	0.89779	0.9222	0.04122	0.0431	0.76609	0.77112	0.49779	0.49305	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36408	36408	SRR546817	SRX180747	SRS358988	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.	pubmed:24531765	Zebrafish wild type AB strain embryo 2 cells stage	D. rerio 2 cells embryo	D. rerio 2 cells embryo			RNAseq D. rerio 2 cells embryo	RNAseq D. rerio 2 cells embryo	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					2799828144.0	18419922.0	RNAseq D. rerio 2 cells embryo	0:76 1:76	A:678251421;C:711410510;G:729905459;T:677312772;N:2947982	76	76	678251421	711410510	729905459	677312772	2947982	SRX180747	SRS358988	SRA055273	University of Bergen	ZEPROME consortium	2	0.9498	0.94704	0.02363	0.02442	0.7988	0.80221	0.48657	0.49361	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	Unknown	2015-07-22	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
36581	36581	SRR594769	SRX195432	SRS369361	SRP016134	PRJNA177654	Danio rerio Transcriptome or Gene expression	PRJNA177654	Other	We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.		1	Test	GFP Negative 1			Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development	Embryos	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016134					2525199228.0	65962848.0	GFP Positive	0:38.28	A:665802914;C:594493287;G:612298433;T:652078696;N:525898	38		665802914	594493287	612298433	652078696	525898	SRX195432	SRS369361			University of Cambridge	1	0.89062		0.09595		0.74059		0.47506		36		B		usable mapping rate	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United Kingdom	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36582	36582	SRR594771	SRX195432	SRS369361	SRP016134	PRJNA177654	Danio rerio Transcriptome or Gene expression	PRJNA177654	Other	We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.		1	Test	GFP Negative 1			Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development	Embryos	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016134			gfp_negative_replicate_1_sequence.txt.gz	fastq	2549682148.0	66546682.0	GFP Negative	0:38.31	A:686329592;C:587342682;G:601330559;T:674194074;N:485241	38		686329592	587342682	601330559	674194074	485241	SRX195432	SRS369361			University of Cambridge	1	0.90413		0.13272		0.71342		0.48186		36		B		usable mapping rate	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United Kingdom	2015-07-22	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
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
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
39751	39751	SRR2422954	SRX1092140	SRS987764	SRP060685	PRJNA289590	Danio rerio Raw sequence reads	PRJNA289590	Whole Genome Sequencing	The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish		U2AFAB KD	U2AFA2B KD	U2A2FA and U2AF2B knockdown		treatment:U2AF2A B morpholino\|developmental stage:embryo\|age:24 hours\|strain:wildtype\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal	U2AF2A and U2AF2B KD	U2AFAB KD	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP060685			zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz	fastq fastq	4010033906.0	19851653.0	u2afa u2afb kd	0:101 1:101	A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449	101	101	954988404	1049486839	1028325376	975960838	1272449	SRX1092140	SRS987764	SRA276795	Brown University\|Fairbrother Lab	Brown University	2	0.88891	0.88704	0.22441	0.2245	0.73781	0.74111	0.60755	0.61314	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
39752	39752	SRR2422968	SRX1092139	SRS987762	SRP060685	PRJNA289590	Danio rerio Raw sequence reads	PRJNA289590	Whole Genome Sequencing	The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish		U2AFB KD	U2AF2B KD	U2AF2B knockdown		treatment:U2AF2B morpholino\|developmental stage:embryo\|age:24 hours\|strain:wildtype\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal	U2AF2B KD	U2AFB KD	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP060685			zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz	fastq fastq	3657236866.0	18105133.0	u2af2b kd	0:101 1:101	A:859906359;C:963846892;G:950183263;T:882292781;N:1007571	101	101	859906359	963846892	950183263	882292781	1007571	SRX1092139	SRS987762	SRA276795	Brown University\|Fairbrother Lab	Brown University	2	0.87685	0.87325	0.21282	0.21347	0.74899	0.75166	0.65013	0.65163	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
39753	39753	SRR2422941	SRX1092136	SRS987760	SRP060685	PRJNA289590	Danio rerio Raw sequence reads	PRJNA289590	Whole Genome Sequencing	The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish		Control1	Control1	Control1		treatment:Control 1\|developmental stage:embryo\|age:24 hours\|strain:wildtype\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal	control 1	Control1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP060685			zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz	fastq fastq	5446154724.0	26961162.0	control1	0:101 1:101	A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287	101	101	1236792250	1484635192	1463483173	1259686822	1557287	SRX1092136	SRS987760	SRA276795	Brown University\|Fairbrother Lab	Brown University	2	0.88645	0.88416	0.23061	0.23167	0.75872	0.75921	0.63459	0.63891	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
39754	39754	SRR2422967	SRX1092138	SRS987763	SRP060685	PRJNA289590	Danio rerio Raw sequence reads	PRJNA289590	Whole Genome Sequencing	The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish		U2AFA KD	U2AF2A KD	U2AF2A knockdown		treatment:U2AF2A morpholino\|developmental stage:embryo\|age:24 hours\|strain:wildtype\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal	U2AF A KD	U2AFA KD	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP060685			zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz	fastq fastq	7385905174.0	36563887.0	u2af2a kd	0:101 1:101	A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609	101	101	1742999157	1956220866	1920103000	1764198542	2383609	SRX1092138	SRS987763	SRA276795	Brown University\|Fairbrother Lab	Brown University	2	0.74404	0.74051	0.14971	0.14762	0.76641	0.76757	0.56197	0.56515	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
39755	39755	SRR2422942	SRX1092137	SRS987761	SRP060685	PRJNA289590	Danio rerio Raw sequence reads	PRJNA289590	Whole Genome Sequencing	The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish		Control2	Control2	Control2		treatment:Control 2\|developmental stage:embryo\|age:24 hours\|strain:wildtype\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal	control 2	Control 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP060685			zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz	fastq fastq	4226478926.0	20923163.0	control2	0:101 1:101	A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890	101	101	1005765442	1098720686	1084955814	1035764094	1272890	SRX1092137	SRS987761	SRA276795	Brown University\|Fairbrother Lab	Brown University	2	0.83225	0.83092	0.22325	0.22374	0.75396	0.75603	0.6203	0.61868	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
39934	39934	SRR2473238	SRX1270438	SRS1078341	SRP063952	PRJNA296414	SPOP mutation leads to genomic instability in prostate cancer	PRJNA296414	Transcriptome Analysis	Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.		Danio rerio embryos ectopically expressing human SPOPwt.		Danio rerio ectopic SPOPwt		strain:AB/T\|age:24 HPF\|sex:pooled male and female\|tissue:whole embryo\|biomaterial provider:Yariv Houvras\|BioSampleModel:Model organism or animal	SPOP mutation leads to genomic instability in prostate cancer	Danio rerio ectopic SPOPwt	1	SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP063952			WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz	fastq fastq	6185345892.0	60640646.0	Danio rerio ectopic SPOPwt	0:51 1:51	A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809	51	51	1647678166	1462773970	1416249443	1657464504	1179809	SRX1270438	SRS1078341			Weill Cornell Medical College	2	0.94598	0.94553	0.09216	0.0934	0.68789	0.69065	0.46814	0.47172	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-02-17	Pharyngula	Embryo	Whole Organism	All anatomical structures
39935	39935	SRR2473236	SRX1270437	SRS1078340	SRP063952	PRJNA296414	SPOP mutation leads to genomic instability in prostate cancer	PRJNA296414	Transcriptome Analysis	Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.		Danio rerio ectopically expressing SPOP F133V		Danio rerio ectopic SPOP F133V		strain:AB/T\|age:24 HPF\|sex:pooled male and female\|tissue:whole embryo\|biomaterial provider:Yariv Houvras\|BioSampleModel:Model organism or animal	SPOP mutation leads to genomic instability in prostate cancer	Danio rerio ectopic SPOP F133V	1	SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP063952			Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz	fastq fastq	6130528134.0	60103217.0	Danio rerio ectopic SPOP F133V	0:51 1:51	A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035	51	51	1630145057	1450811256	1409924927	1638457859	1189035	SRX1270437	SRS1078340			Weill Cornell Medical College	2	0.9444	0.94139	0.09809	0.0979	0.68487	0.68657	0.46751	0.47276	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-09-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
39936	39936	SRR2473235	SRX1270436	SRS1078339	SRP063952	PRJNA296414	SPOP mutation leads to genomic instability in prostate cancer	PRJNA296414	Transcriptome Analysis	Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.				Danio rerio SPOP morpholino		strain:AB/T\|age:24 HPF\|sex:pooled male and female\|tissue:whole embryo\|biomaterial provider:Yariv Houvras\|BioSampleModel:Model organism or animal	Danio rerio SPOP morpholino	Danio rerio SPOP morpholino	1	SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP063952			Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz	fastq fastq	5693947938.0	55823019.0	Danio rerio SPOP morpholino	0:51 1:51	A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641	51	51	1513477521	1350461483	1305374194	1523527099	1107641	SRX1270436	SRS1078339			Weill Cornell Medical College	2	0.94534	0.94431	0.09368	0.0945	0.68941	0.69077	0.46543	0.46749	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-02-17	Pharyngula	Embryo	Whole Organism	All anatomical structures
40711	40711	SRR3420419	SRX1660357	SRS1360318	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00719 8h 2		strain:TUAB\|age:8h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CGATGT\|BioSampleModel:Model organism or animal	AG00719 8h 2	AG00719 8h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz	fastq fastq	2419781176.0	15919613.0	AG00719 run 1	0:76 1:76	A:738997601;C:465047900;G:477140497;T:733241052;N:5354126	76	76	738997601	465047900	477140497	733241052	5354126	SRX1660357	SRS1360318	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.78184	0.71182	0.66469	0.60037	0.75743	0.77518	0.53432	0.52801	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40712	40712	SRR3420420	SRX1660357	SRS1360318	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00719 8h 2		strain:TUAB\|age:8h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CGATGT\|BioSampleModel:Model organism or animal	AG00719 8h 2	AG00719 8h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz	fastq fastq	3074724552.0	20228451.0	AG00719 run 2	0:76 1:76	A:918671897;C:609510609;G:622542852;T:922439528;N:1559666	76	76	918671897	609510609	622542852	922439528	1559666	SRX1660357	SRS1360318	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.76444	0.65488	0.65157	0.55185	0.75741	0.78106	0.53067	0.52622	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40713	40713	SRR3420421	SRX1660357	SRS1360318	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00719 8h 2		strain:TUAB\|age:8h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CGATGT\|BioSampleModel:Model organism or animal	AG00719 8h 2	AG00719 8h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz	fastq fastq	2666395856.0	17542078.0	AG00719 run 3	0:76 1:76	A:787508876;C:539791618;G:549145516;T:785088342;N:4861504	76	76	787508876	539791618	549145516	785088342	4861504	SRX1660357	SRS1360318	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.75479	0.69465	0.63843	0.58422	0.75716	0.78423	0.53952	0.52615	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40714	40714	SRR3420388	SRX1660356	SRS1360315	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00718 8h 1		strain:TUAB\|age:8h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ATCACG\|BioSampleModel:Model organism or animal	AG00718 8h 1	AG00718 8h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz	fastq fastq	2699903800.0	17762525.0	AG00718 run 1	0:76 1:76	A:832300161;C:503956886;G:525141498;T:832566681;N:5938574	76	76	832300161	503956886	525141498	832566681	5938574	SRX1660356	SRS1360315	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.76651	0.69033	0.63937	0.56749	0.77145	0.78545	0.53429	0.53165	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40715	40715	SRR3420392	SRX1660356	SRS1360315	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00718 8h 1		strain:TUAB\|age:8h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ATCACG\|BioSampleModel:Model organism or animal	AG00718 8h 1	AG00718 8h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz	fastq fastq	2798947456.0	18414128.0	AG00718 run 2	0:76 1:76	A:853546590;C:536347349;G:556751964;T:851863324;N:438229	76	76	853546590	536347349	556751964	851863324	438229	SRX1660356	SRS1360315	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.74665	0.63683	0.6265	0.5237	0.76134	0.7905	0.54613	0.53982	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-04-22	Gastrula	Embryo	Whole Organism	All anatomical structures
40716	40716	SRR3420398	SRX1660355	SRS1360316	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00717 6h 2		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CTTGTA\|BioSampleModel:Model organism or animal	AG00717 6h 2	AG00717 6h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz	fastq fastq	1442918520.0	9492885.0	AG00717 run 1	0:76 1:76	A:442675510;C:273265985;G:284514997;T:439403136;N:3058892	76	76	442675510	273265985	284514997	439403136	3058892	SRX1660355	SRS1360316	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.76736	0.69048	0.60693	0.53532	0.74647	0.76138	0.51546	0.5135	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40717	40717	SRR3420402	SRX1660355	SRS1360316	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00717 6h 2		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CTTGTA\|BioSampleModel:Model organism or animal	AG00717 6h 2	AG00717 6h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz	fastq fastq	2524099688.0	16605919.0	AG00717 run 2	0:76 1:76	A:752163917;C:500880325;G:526291920;T:744462824;N:300702	76	76	752163917	500880325	526291920	744462824	300702	SRX1660355	SRS1360316	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.7274	0.651	0.57791	0.50498	0.74434	0.76329	0.51831	0.50479	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40718	40718	SRR3420405	SRX1660355	SRS1360316	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00717 6h 2		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CTTGTA\|BioSampleModel:Model organism or animal	AG00717 6h 2	AG00717 6h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz	fastq fastq	1320586032.0	8688066.0	AG00717 run 3	0:76 1:76	A:394339370;C:259687848;G:270914284;T:389960707;N:5683823	76	76	394339370	259687848	270914284	389960707	5683823	SRX1660355	SRS1360316	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.72219	0.6734	0.55665	0.5122	0.75371	0.76323	0.5098	0.50658	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40719	40719	SRR3420409	SRX1660355	SRS1360316	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00717 6h 2		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CTTGTA\|BioSampleModel:Model organism or animal	AG00717 6h 2	AG00717 6h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz	fastq fastq	1778143272.0	11698311.0	AG00717 run 4	0:76 1:76	A:531893644;C:351009327;G:366187476;T:528937189;N:115636	76	76	531893644	351009327	366187476	528937189	115636	SRX1660355	SRS1360316	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.72027	0.6573	0.57252	0.50814	0.74913	0.77479	0.51537	0.50066	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40720	40720	SRR3420315	SRX1660354	SRS1360300	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00716 6h 1		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GATCAG\|BioSampleModel:Model organism or animal	AG00716 6h 1	AG00716 6h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz	fastq fastq	1837024424.0	12085687.0	AG00716 run 1	0:76 1:76	A:571581150;C:339887376;G:357200726;T:564453542;N:3901630	76	76	571581150	339887376	357200726	564453542	3901630	SRX1660354	SRS1360300	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.77818	0.69777	0.64211	0.56481	0.75503	0.76926	0.50584	0.51507	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40721	40721	SRR3420319	SRX1660354	SRS1360300	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00716 6h 1		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GATCAG\|BioSampleModel:Model organism or animal	AG00716 6h 1	AG00716 6h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz	fastq fastq	2763994600.0	18184175.0	AG00716 run 2	0:76 1:76	A:841712204;C:530711238;G:562110067;T:828853061;N:608030	76	76	841712204	530711238	562110067	828853061	608030	SRX1660354	SRS1360300	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.74716	0.66787	0.61425	0.53764	0.7475	0.76518	0.50855	0.51311	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-04-22	Gastrula	Embryo	Whole Organism	All anatomical structures
40722	40722	SRR3420323	SRX1660354	SRS1360300	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00716 6h 1		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GATCAG\|BioSampleModel:Model organism or animal	AG00716 6h 1	AG00716 6h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz	fastq fastq	1055704904.0	6945427.0	AG00716 run 3	0:76 1:76	A:323142351;C:199674907;G:210508599;T:317806564;N:4572483	76	76	323142351	199674907	210508599	317806564	4572483	SRX1660354	SRS1360300	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.73664	0.68701	0.59387	0.5447	0.76179	0.76132	0.51299	0.51552	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
40723	40723	SRR3420327	SRX1660354	SRS1360300	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00716 6h 1		strain:TUAB\|age:6h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GATCAG\|BioSampleModel:Model organism or animal	AG00716 6h 1	AG00716 6h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz	fastq fastq	2526928408.0	16624529.0	AG00716 run 4	0:76 1:76	A:771333886;C:482964782;G:508687112;T:763609426;N:333202	76	76	771333886	482964782	508687112	763609426	333202	SRX1660354	SRS1360300	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.74535	0.66478	0.61452	0.53584	0.75826	0.77329	0.51139	0.51539	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-04-22	Gastrula	Embryo	Whole Organism	All anatomical structures
40724	40724	SRR3420333	SRX1660350	SRS1360304	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00715 4h 2		strain:TUAB\|age:4h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CAGATC\|BioSampleModel:Model organism or animal	AG00715 4h 2	AG00715 4h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz	fastq fastq	2314408088.0	15226369.0	AG00715 run 1	0:76 1:76	A:652783335;C:485705748;G:507451689;T:663544778;N:4922538	76	76	652783335	485705748	507451689	663544778	4922538	SRX1660350	SRS1360304	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.59859	0.55293	0.24175	0.21943	0.78384	0.79174	0.52173	0.52111	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40725	40725	SRR3420337	SRX1660350	SRS1360304	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00715 4h 2		strain:TUAB\|age:4h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CAGATC\|BioSampleModel:Model organism or animal	AG00715 4h 2	AG00715 4h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz	fastq fastq	2461668424.0	16195187.0	AG00715 run 2	0:76 1:76	A:653884256;C:562168304;G:597853484;T:647470498;N:291882	76	76	653884256	562168304	597853484	647470498	291882	SRX1660350	SRS1360304	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.5374	0.51402	0.2167	0.19427	0.78575	0.7934	0.52714	0.53043	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40726	40726	SRR3420341	SRX1660350	SRS1360304	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00715 4h 2		strain:TUAB\|age:4h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CAGATC\|BioSampleModel:Model organism or animal	AG00715 4h 2	AG00715 4h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz	fastq fastq	3692351624.0	24291787.0	AG00715 run 3	0:76 1:76	A:984283909;C:835828915;G:881112020;T:975490829;N:15635951	76	76	984283909	835828915	881112020	975490829	15635951	SRX1660350	SRS1360304	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.54752	0.52404	0.18037	0.16908	0.79358	0.7961	0.50982	0.50975	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40727	40727	SRR3420346	SRX1660346	SRS1360308	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00714 4h 1		strain:TUAB\|age:4h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GCCAAT\|BioSampleModel:Model organism or animal	AG00714 4h 1	AG00714 4h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz	fastq fastq	2377192296.0	15639423.0	AG00714 run 1	0:76 1:76	A:694380135;C:473427723;G:496920379;T:707435115;N:5028944	76	76	694380135	473427723	496920379	707435115	5028944	SRX1660346	SRS1360308	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.69444	0.63521	0.40011	0.36148	0.76252	0.77116	0.50751	0.5108	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40728	40728	SRR3420349	SRX1660346	SRS1360308	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00714 4h 1		strain:TUAB\|age:4h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:GCCAAT\|BioSampleModel:Model organism or animal	AG00714 4h 1	AG00714 4h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz	fastq fastq	1841902256.0	12117778.0	AG00714 run 2	0:76 1:76	A:517451432;C:392444197;G:415696773;T:508506741;N:7803113	76	76	517451432	392444197	415696773	508506741	7803113	SRX1660346	SRS1360308	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.63625	0.60304	0.3341	0.31189	0.77224	0.77703	0.50754	0.51039	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40729	40729	SRR3420359	SRX1660342	SRS1360312	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00713 3h 2		strain:TUAB\|age:3h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ACAGTG\|BioSampleModel:Model organism or animal	AG00713 3h 2	AG00713 3h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz	fastq fastq	2674764976.0	17597138.0	AG00713 run 1	0:76 1:76	A:738399424;C:560443522;G:578733188;T:791450319;N:5738523	76	76	738399424	560443522	578733188	791450319	5738523	SRX1660342	SRS1360312	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.63595	0.60509	0.17579	0.17695	0.79066	0.79815	0.49657	0.4916	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40730	40730	SRR3420362	SRX1660342	SRS1360312	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00713 3h 2		strain:TUAB\|age:3h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ACAGTG\|BioSampleModel:Model organism or animal	AG00713 3h 2	AG00713 3h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz	fastq fastq	2463895376.0	16209838.0	AG00713 run 2	0:76 1:76	A:661360403;C:556078326;G:581335469;T:654625128;N:10496050	76	76	661360403	556078326	581335469	654625128	10496050	SRX1660342	SRS1360312	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.58767	0.56878	0.14864	0.14485	0.79476	0.79898	0.49508	0.49769	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40731	40731	SRR3420369	SRX1660341	SRS1360313	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00712 3h 1		strain:TUAB\|age:3h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:TGACCA\|BioSampleModel:Model organism or animal	AG00712 3h 1	AG00712 3h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz	fastq fastq	1354427464.0	8910707.0	AG00712 run 1	0:76 1:76	A:382647488;C:281900295;G:291990859;T:395032379;N:2856443	76	76	382647488	281900295	291990859	395032379	2856443	SRX1660341	SRS1360313	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.64156	0.60052	0.23835	0.22296	0.78025	0.78717	0.49813	0.49898	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40732	40732	SRR3420375	SRX1660341	SRS1360313	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00712 3h 1		strain:TUAB\|age:3h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:TGACCA\|BioSampleModel:Model organism or animal	AG00712 3h 1	AG00712 3h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz	fastq fastq	2335782480.0	15366990.0	AG00712 run 2	0:76 1:76	A:638971995;C:517112038;G:538588809;T:640731763;N:377875	76	76	638971995	517112038	538588809	640731763	377875	SRX1660341	SRS1360313	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.60525	0.56571	0.24772	0.21069	0.77043	0.78543	0.50862	0.50386	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40733	40733	SRR3420379	SRX1660340	SRS1360314	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00711 2.5h 2		strain:TUAB\|age:2.5h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CGATGT\|BioSampleModel:Model organism or animal	AG00711 2.5h 2	AG00711 2.5h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz	fastq fastq	2343343264.0	15416732.0	AG00711 run 1	0:76 1:76	A:645206414;C:505367235;G:523792864;T:663977432;N:4999319	76	76	645206414	505367235	523792864	663977432	4999319	SRX1660340	SRS1360314	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.59395	0.56211	0.10259	0.10243	0.80598	0.80911	0.51352	0.53772	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40734	40734	SRR3420383	SRX1660340	SRS1360314	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00711 2.5h 2		strain:TUAB\|age:2.5h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:CGATGT\|BioSampleModel:Model organism or animal	AG00711 2.5h 2	AG00711 2.5h 2	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz	fastq fastq	2668460776.0	17555663.0	AG00711 run 2	0:76 1:76	A:709820753;C:602900273;G:626554840;T:717828006;N:11356904	76	76	709820753	602900273	626554840	717828006	11356904	SRX1660340	SRS1360314	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.56281	0.54232	0.09217	0.09047	0.80657	0.81018	0.50757	0.52507	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40735	40735	SRR3420304	SRX1660339	SRS1360299	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00710 2.5h 1		strain:TUAB\|age:2.5h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ATCACG\|BioSampleModel:Model organism or animal	AG00710 2.5h 1	AG00710 2.5h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz	fastq fastq	2705199784.0	17797367.0	AG00710 run 1	0:76 1:76	A:737065338;C:573787464;G:595216660;T:793361986;N:5768336	76	76	737065338	573787464	595216660	793361986	5768336	SRX1660339	SRS1360299	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.60426	0.58122	0.08196	0.09224	0.80578	0.8075	0.50121	0.50121	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
40736	40736	SRR3420308	SRX1660339	SRS1360299	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.				AG00710 2.5h 1		strain:TUAB\|age:2.5h\|sex:pooled male and female\|tissue:whole embryo\|treatment:alpha amanitin\|barcode:ATCACG\|BioSampleModel:Model organism or animal	AG00710 2.5h 1	AG00710 2.5h 1	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz	fastq fastq	2275540168.0	14970659.0	AG00710 run 2	0:76 1:76	A:614429428;C:505827101;G:528906356;T:616697803;N:9679480	76	76	614429428	505827101	528906356	616697803	9679480	SRX1660339	SRS1360299	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.57792	0.56382	0.07268	0.07246	0.80261	0.80612	0.49743	0.50296	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Blastula	Embryo	Whole Organism	All anatomical structures
41381	41381	SRR4375307	SRX2226800	SRS1732678	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B1	resa AG01072		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B1	AG01072.1	AG01072.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz	fastq fastq	756436968.0	4976559.0	AG01072.1 R2.fastq.gz	0:76 1:76	A:277813562;C:101592220;G:103435859;T:273576694;N:18633	76	76	277813562	101592220	103435859	273576694	18633	SRX2226800	SRS1732678	SRA482696	Yale University\|Genetics	Yale University	2	0.00777	0.00795	0.00043	0.00056	0.99344	0.99389	0.43869	0.43095	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-10-06	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41382	41382	SRR4375306	SRX2226799	SRS1732692	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h pA r3 B3	resa AG01070		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B3	AG01070.1	AG01070.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz	fastq fastq	601712368.0	3958634.0	AG01070.1 R2.fastq.gz	0:76 1:76	A:188474921;C:113643606;G:114382568;T:185195364;N:15909	76	76	188474921	113643606	114382568	185195364	15909	SRX2226799	SRS1732692	SRA482696	Yale University\|Genetics	Yale University	2	0.84037	0.84016	0.03493	0.03544	0.97303	0.97252	0.46337	0.47093	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41383	41383	SRR4375305	SRX2226798	SRS1732691	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h pA r3 B2	resa AG01069		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B2	AG01069.1	AG01069.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz	fastq fastq	1344477848.0	8845249.0	AG01069.1 R1.fastq.gz	0:76 1:76	A:418545593;C:256422789;G:257715519;T:411760293;N:33654	76	76	418545593	256422789	257715519	411760293	33654	SRX2226798	SRS1732691	SRA482696	Yale University\|Genetics	Yale University	2	0.84542	0.84566	0.03642	0.03588	0.97084	0.97197	0.4739	0.48121	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41384	41384	SRR4375304	SRX2226797	SRS1732690	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h pA r3 B1	resa AG01068		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 8h pA r3 B1	AG01068.1	AG01068.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz	fastq fastq	896200056.0	5896053.0	AG01068.1 R2.fastq.gz	0:76 1:76	A:278768309;C:171161843;G:172303088;T:273944252;N:22564	76	76	278768309	171161843	172303088	273944252	22564	SRX2226797	SRS1732690	SRA482696	Yale University\|Genetics	Yale University	2	0.83862	0.83897	0.0351	0.03585	0.97183	0.97204	0.47364	0.47138	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41385	41385	SRR4375303	SRX2226796	SRS1732689	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h L430 pA r3 B3	resa AG01067		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B3	AG01067.1	AG01067.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz	fastq fastq	1799778192.0	11840646.0	AG01067.1 R1.fastq.gz	0:76 1:76	A:561491448;C:342221462;G:343998479;T:552022535;N:44268	76	76	561491448	342221462	343998479	552022535	44268	SRX2226796	SRS1732689	SRA482696	Yale University\|Genetics	Yale University	2	0.84432	0.84397	0.03554	0.03522	0.97224	0.9725	0.46732	0.46922	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41386	41386	SRR4375302	SRX2226795	SRS1732688	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h L430 pA r3 B2	resa AG01066		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B2	AG01066.1	AG01066.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz	fastq fastq	1313436864.0	8641032.0	AG01066.1 R2.fastq.gz	0:76 1:76	A:409666264;C:249755645;G:251028600;T:402953610;N:32745	76	76	409666264	249755645	251028600	402953610	32745	SRX2226795	SRS1732688	SRA482696	Yale University\|Genetics	Yale University	2	0.84584	0.84611	0.0349	0.03543	0.97189	0.97175	0.47547	0.48555	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41387	41387	SRR4375301	SRX2226794	SRS1732687	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 8h L430 pA r3 B1	resa AG01065		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr tinyLNA miR 430\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 8h L430 pA r3 B1	AG01065.1	AG01065.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz	fastq fastq	1442385152.0	9489376.0	AG01065.1 R2.fastq.gz	0:76 1:76	A:449362282;C:274879749;G:276626223;T:441480173;N:36725	76	76	449362282	274879749	276626223	441480173	36725	SRX2226794	SRS1732687	SRA482696	Yale University\|Genetics	Yale University	2	0.8417	0.84205	0.03519	0.03559	0.97193	0.97179	0.47697	0.46118	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41388	41388	SRR4375300	SRX2226793	SRS1732685	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA CLIP Ago2 RESA CLIP Ago2 input	resa clip ago2 AG01631		strain:TU/AB\|age:4.7\|dev stage:zfs:0000015\|sex:pooled male and female\|tissue:embryo\|treatment:500UTR flag ago2 crosslink\|molecule:RNA\|selection:5% input before pulldown\|condition:input\|BioSampleModel:Model organism or animal	RESA CLIP Ago2 RESA CLIP Ago2 input	AG01631.1	AG01631.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz	fastq fastq	9864834960.0	64900230.0	AG01631.1 R2.fastq.gz	0:76 1:76	A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520	76	76	2990534603	1958949912	1963153108	2951932817	264520	SRX2226793	SRS1732685	SRA482696	Yale University\|Genetics	Yale University	2	0.83121	0.85078	0.03505	0.0364	0.97171	0.97019	0.46925	0.47246	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41389	41389	SRR4375299	SRX2226779	SRS1732684	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA CLIP Ago2 RESA CLIP Ago2 IP	resa clip ago2 AG01630		strain:TU/AB\|age:4.7\|dev stage:zfs:0000015\|sex:pooled male and female\|tissue:embryo\|treatment:500UTR flag ago2 crosslink\|molecule:RNA\|selection:flag bead pulldown post crosslinking\|condition:Ago2 IP\|BioSampleModel:Model organism or animal	RESA CLIP Ago2 RESA CLIP Ago2 IP	AG01630.1	AG01630.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz	fastq fastq	9348207632.0	61501366.0	AG01630.1 R1.fastq.gz	0:76 1:76	A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848	76	76	2819572908	1871537719	1881735941	2775115216	245848	SRX2226779	SRS1732684	SRA482696	Yale University\|Genetics	Yale University	2	0.80207	0.78648	0.02992	0.02839	0.97885	0.97871	0.49297	0.49107	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41390	41390	SRR4375197	SRX2226727	SRS1732683	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B3	resa AG01086		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B3	AG01086.2	AG01086.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz	fastq fastq	714848400.0	4702950.0	AG01086.2 R2.fastq.gz	0:76 1:76	A:261928616;C:96586565;G:97768464;T:258351392;N:213363	76	76	261928616	96586565	97768464	258351392	213363	SRX2226727	SRS1732683	SRA482696	Yale University\|Genetics	Yale University	2	0.00715	0.00733	0.00046	0.00044	0.99417	0.99435	0.46775	0.42207	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41391	41391	SRR4375176	SRX2226710	SRS1732686	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 64c pA r3 B2	resa AG01061		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq WT 64c pA r3 B2	AG01061.1	AG01061.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz	fastq fastq	724448416.0	4766108.0	AG01061.1 R2.fastq.gz	0:76 1:76	A:224701149;C:138989041;G:139762199;T:220977796;N:18231	76	76	224701149	138989041	139762199	220977796	18231	SRX2226710	SRS1732686	SRA482696	Yale University\|Genetics	Yale University	2	0.84913	0.84756	0.03557	0.03568	0.97153	0.97116	0.47281	0.46157	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-10-06	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41392	41392	SRR4375175	SRX2226709	SRS1732683	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B3	resa AG01086		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B3	AG01086.1	AG01086.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz	fastq fastq	411922128.0	2710014.0	AG01086.1 R1.fastq.gz	0:76 1:76	A:150812258;C:55795177;G:56809368;T:148495332;N:9993	76	76	150812258	55795177	56809368	148495332	9993	SRX2226709	SRS1732683	SRA482696	Yale University\|Genetics	Yale University	2	0.00798	0.00746	0.00062	0.00055	0.99385	0.99399	0.44328	0.47308	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41393	41393	SRR4375146	SRX2226694	SRS1732682	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B2	resa AG01085		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B2	AG01085.2	AG01085.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz	fastq fastq	700337720.0	4607485.0	AG01085.2 R1.fastq.gz	0:76 1:76	A:256568404;C:94627005;G:95783677;T:253149693;N:208941	76	76	256568404	94627005	95783677	253149693	208941	SRX2226694	SRS1732682	SRA482696	Yale University\|Genetics	Yale University	2	0.00733	0.00726	0.00055	0.00048	0.99413	0.99393	0.46893	0.45795	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41394	41394	SRR4375102	SRX2226674	SRS1732682	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B2	resa AG01085		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B2	AG01085.1	AG01085.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz	fastq fastq	409587712.0	2694656.0	AG01085.1 R1.fastq.gz	0:76 1:76	A:149931448;C:55481183;G:56493706;T:147671446;N:9929	76	76	149931448	55481183	56493706	147671446	9929	SRX2226674	SRS1732682	SRA482696	Yale University\|Genetics	Yale University	2	0.0079	0.0078	0.00056	0.0005	0.99366	0.99385	0.42647	0.47214	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41395	41395	SRR4375101	SRX2226673	SRS1732681	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B1	resa AG01084		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B1	AG01084.2	AG01084.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz	fastq fastq	396825488.0	2610694.0	AG01084.2 R1.fastq.gz	0:76 1:76	A:145317384;C:53679748;G:54375412;T:143331621;N:121323	76	76	145317384	53679748	54375412	143331621	121323	SRX2226673	SRS1732681	SRA482696	Yale University\|Genetics	Yale University	2	0.0071	0.00673	0.00044	0.00042	0.99417	0.99419	0.44659	0.45357	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41396	41396	SRR4375100	SRX2226672	SRS1732681	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 8h B1	resa AG01084		strain:TU/AB\|age:8.0\|dev stage:75% epiboly\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 8h B1	AG01084.1	AG01084.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz	fastq fastq	236514888.0	1556019.0	AG01084.1 R1.fastq.gz	0:76 1:76	A:86560104;C:32062698;G:32664624;T:85221432;N:6030	76	76	86560104	32062698	32664624	85221432	6030	SRX2226672	SRS1732681	SRA482696	Yale University\|Genetics	Yale University	2	0.00756	0.00706	0.00061	0.00064	0.99405	0.99419	0.47228	0.48736	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41397	41397	SRR4375099	SRX2226671	SRS1732680	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B3	resa AG01074		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B3	AG01074.2	AG01074.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz	fastq fastq	1411678568.0	9287359.0	AG01074.2 R1.fastq.gz	0:76 1:76	A:518452828;C:189515599;G:191777773;T:511511925;N:420443	76	76	518452828	189515599	191777773	511511925	420443	SRX2226671	SRS1732680	SRA482696	Yale University\|Genetics	Yale University	2	0.00745	0.00729	0.00047	0.00045	0.99405	0.99411	0.43814	0.47981	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41398	41398	SRR4375098	SRX2226670	SRS1732680	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B3	resa AG01074		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:3\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B3	AG01074.1	AG01074.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01074.1_R1.fastq.gz AG01074.1_R2.fastq.gz	fastq fastq	867077312.0	5704456.0	AG01074.1 R1.fastq.gz	0:76 1:76	A:318238609;C:116633576;G:118737324;T:313446459;N:21344	76	76	318238609	116633576	118737324	313446459	21344	SRX2226670	SRS1732680	SRA482696	Yale University\|Genetics	Yale University	2	0.00791	0.00753	0.00052	0.00054	0.99395	0.99381	0.45038	0.44477	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41399	41399	SRR4375097	SRX2226669	SRS1732679	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B2	resa AG01073		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B2	AG01073.2	AG01073.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01073.2_R1.fastq.gz AG01073.2_R2.fastq.gz	fastq fastq	1170921968.0	7703434.0	AG01073.2 R1.fastq.gz	0:76 1:76	A:430252673;C:156958676;G:158824982;T:424542052;N:343585	76	76	430252673	156958676	158824982	424542052	343585	SRX2226669	SRS1732679	SRA482696	Yale University\|Genetics	Yale University	2	0.00759	0.00753	0.00044	0.00046	0.99389	0.99375	0.48023	0.49305	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41400	41400	SRR4375096	SRX2226668	SRS1732679	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B2	resa AG01073		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:2\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B2	AG01073.1	AG01073.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01073.1_R1.fastq.gz AG01073.1_R2.fastq.gz	fastq fastq	650729936.0	4281118.0	AG01073.1 R1.fastq.gz	0:76 1:76	A:238957997;C:87418913;G:88996057;T:235340339;N:16630	76	76	238957997	87418913	88996057	235340339	16630	SRX2226668	SRS1732679	SRA482696	Yale University\|Genetics	Yale University	2	0.00771	0.00754	0.00052	0.00049	0.99403	0.9936	0.46484	0.42136	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41401	41401	SRR4375095	SRX2226667	SRS1732678	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Mut 64c B1	resa AG01072		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr HSO3\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq Mut 64c B1	AG01072.2	AG01072.2	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01072.2_R1.fastq.gz AG01072.2_R2.fastq.gz	fastq fastq	1293717904.0	8511302.0	AG01072.2 R1.fastq.gz	0:76 1:76	A:475476006;C:173352933;G:175448573;T:469059516;N:380876	76	76	475476006	173352933	175448573	469059516	380876	SRX2226667	SRS1732678	SRA482696	Yale University\|Genetics	Yale University	2	0.0072	0.0071	0.00042	0.00038	0.99397	0.99385	0.4403	0.43351	76	76	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
41402	41402	SRR4375094	SRX2226666	SRS1732677	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq WT 64c pA r3 B1	resa AG01060		strain:TU/AB\|age:2.0\|dev stage:64c\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|selection:pA\|replicate:1\|BioSampleModel:Model organism or animal	RESA Seq WT 64c pA r3 B1	AG01060.1	AG01060.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG01060.1_R1.fastq.gz AG01060.1_R2.fastq.gz	fastq fastq	531097120.0	3494060.0	AG01060.1 R1.fastq.gz	0:76 1:76	A:164891814;C:101739900;G:102440303;T:162011179;N:13924	76	76	164891814	101739900	102440303	162011179	13924	SRX2226666	SRS1732677	SRA482696	Yale University\|Genetics	Yale University	2	0.84523	0.84587	0.03561	0.03503	0.9723	0.97161	0.46204	0.47901	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41403	41403	SRR4375093	SRX2226665	SRS1732676	SRP090954	PRJNA345638	RESA identifies mRNA regulatory sequences with high resolution	PRJNA345638	Other	Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.			RESA Seq Needle r2	resa AG00580		strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|treatment:500utr\|molecule:RNA\|condition:needle\|BioSampleModel:Model organism or animal	RESA Seq Needle r2	AG00580.1	AG00580.1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP090954			AG00580.1_R1.fastq.gz AG00580.1_R2.fastq.gz	fastq fastq	536691936.0	3530868.0	AG00580.1 R1.fastq.gz	0:76 1:76	A:162711942;C:106417027;G:106484569;T:160130705;N:947693	76	76	162711942	106417027	106484569	160130705	947693	SRX2226665	SRS1732676	SRA482696	Yale University\|Genetics	Yale University	2	0.85835	0.85877	0.03686	0.03615	0.96818	0.96895	0.47111	0.47948	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-12-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
42492	42492	SRR5681431	SRX2916758	SRS2282896	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				15um		strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:15um\|BioSampleModel:Model organism or animal	15um zebrafish	15um zebrafish	15um zebrafish	15um zebrafish			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143			15um_2.fq.gz 15um_1.fq.gz	fastq fastq	4510379400.0	22551897.0	15um 2.fq.gz	0:100 1:100	A:1183709237;C:1078933188;G:1057042534;T:1190615427;N:79014	100	100	1183709237	1078933188	1057042534	1190615427	79014	SRX2916758	SRS2282896	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.95073	0.95055	0.0647	0.06526	0.67176	0.67351	0.46247	0.46176	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
42493	42493	SRR5681432	SRX2916757	SRS2282895	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				10um		strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:10um\|BioSampleModel:Model organism or animal	10um zebrafish	10um zebrafish	10um zebrafish	10um zebrafish			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143			10um_1.fq.gz 10um_2.fq.gz	fastq fastq	4513300800.0	22566504.0	10um 1.fq.gz	0:100 1:100	A:1186008993;C:1078123999;G:1056044415;T:1193043558;N:79835	100	100	1186008993	1078123999	1056044415	1193043558	79835	SRX2916757	SRS2282895	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.94799	0.94687	0.07002	0.06979	0.66667	0.66746	0.47255	0.47338	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
42494	42494	SRR5681433	SRX2916756	SRS2282894	SRP109143	PRJNA389374	Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis	PRJNA389374	Whole Genome Sequencing	the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.				control		strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|sex:not determined\|tissue:embryos\|treatment:control\|BioSampleModel:Model organism or animal	control zebrafish	control zebrafish	control zebrafish	control zebrafish			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP109143			con_1.fq.gz con_2.fq.gz	fastq fastq	4514603400.0	22573017.0	con 2.fq.gz	0:100 1:100	A:1183878943;C:1081336890;G:1058805201;T:1190503424;N:78942	100	100	1183878943	1081336890	1058805201	1190503424	78942	SRX2916756	SRS2282894	SRA574072	The Chinese University of HongKong\|School of Biomedical Sciences	The Chinese University of HongKong	2	0.951	0.95009	0.0669	0.06735	0.6659	0.66681	0.46599	0.46703	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	China	2017-06-14	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
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

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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");;