metadata: run_metadata: 942 rows where experiment.library_selection = "unspecified", experiment.library_source = "TRANSCRIPTOMIC" and experiment.platform = "ILLUMINA"

942 rows where experiment.library_selection = "unspecified", experiment.library_source = "TRANSCRIPTOMIC" and experiment.platform = "ILLUMINA"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_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
8059	8059	ERR022480	ERX008923	ERS000088	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other					ZF female head sample1	SAMEA708836	Wellcome Sanger Institute	Alias:ZF female head sample1\|Description:RNA extracted from female adult zebrafish head\|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:ERS000088\|Sample Name:ERS000088\|Sex:female\|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 adult female head	RNA from Zebrafish adult female head	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: DEVELPOMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head	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_5.srf	srf	1622590272.0	15023984.0	E MTAB 434:2719 5.srf	0:54 1:54	A:426435544;C:373743071;G:387589492;T:432086510;N:2735655	54	54	426435544	373743071	387589492	432086510	2735655	ERX008923	ERS000088	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.94624	0.94338	0.17949	0.17965	0.66454	0.66872	0.51097	0.51377	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
8060	8060	ERR022481	ERX008923	ERS000088	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other					ZF female head sample1	SAMEA708836	Wellcome Sanger Institute	Alias:ZF female head sample1\|Description:RNA extracted from female adult zebrafish head\|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:ERS000088\|Sample Name:ERS000088\|Sex:female\|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 adult female head	RNA from Zebrafish adult female head	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: DEVELPOMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head	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_6.srf	srf	1693460736.0	15680192.0	E MTAB 434:2719 6.srf	0:54 1:54	A:445666325;C:389360280;G:403789644;T:451529226;N:3115261	54	54	445666325	389360280	403789644	451529226	3115261	ERX008923	ERS000088	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.94579	0.94429	0.17895	0.17923	0.66864	0.67164	0.51788	0.51083	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
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
9982	9982	ERR4568390	ERX4504063	ERS5050806	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Proximal Rep3	SAMEA7292236	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292236\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Proximal Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Proximal Rep3\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Proximal Rep3 p	HypoTH Proximal Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HP3_CRRA200004859-1a_HV532DSXX_L4_1.fq.gz HP3_CRRA200004859-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7117020000.0	23723400.0	E MTAB 9528:HP3 CRRA200004859 1a HV532DSXX L4	0:150 1:150	A:1864896771;C:1704008842;G:1704487221;T:1843451594;N:175572	150	150	1864896771	1704008842	1704487221	1843451594	175572	ERX4504063	ERS5050806	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.94335	0.9433	0.08657	0.08625	0.72498	0.72636	0.48274	0.4859	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9983	9983	ERR4568389	ERX4504062	ERS5050805	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Proximal Rep2	SAMEA7292235	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292235\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Proximal Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Proximal Rep2\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Proximal Rep2 p	HypoTH Proximal Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HP2_CRRA200004858-1a_HV532DSXX_L4_1.fq.gz HP2_CRRA200004858-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7810736700.0	26035789.0	E MTAB 9528:HP2 CRRA200004858 1a HV532DSXX L4	0:150 1:150	A:2064202307;C:1840783570;G:1863746983;T:2041812726;N:191114	150	150	2064202307	1840783570	1863746983	2041812726	191114	ERX4504062	ERS5050805	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93642	0.93627	0.08781	0.08757	0.72841	0.72872	0.48431	0.48311	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9984	9984	ERR4568388	ERX4504061	ERS5050804	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Proximal Rep1	SAMEA7292234	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292234\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Proximal Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Proximal Rep1\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Proximal Rep1 p	HypoTH Proximal Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HP1_CRRA200004857-1a_HV532DSXX_L4_1.fq.gz HP1_CRRA200004857-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7143318600.0	23811062.0	E MTAB 9528:HP1 CRRA200004857 1a HV532DSXX L4	0:150 1:150	A:1883244963;C:1695388732;G:1697412462;T:1867096015;N:176428	150	150	1883244963	1695388732	1697412462	1867096015	176428	ERX4504061	ERS5050804	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.9408	0.94186	0.08491	0.08465	0.73129	0.73099	0.47185	0.47442	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9985	9985	ERR4568387	ERX4504060	ERS5050803	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Proximal Rep3	SAMEA7292233	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292233\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Proximal Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Proximal Rep3\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Proximal Rep3 p	EuTH Proximal Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EP3_CRRA200004850-1a_HV532DSXX_L4_1.fq.gz EP3_CRRA200004850-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7860809700.0	26202699.0	E MTAB 9528:EP3 CRRA200004850 1a HV532DSXX L4	0:150 1:150	A:2068735854;C:1871645002;G:1876330645;T:2043901317;N:196882	150	150	2068735854	1871645002	1876330645	2043901317	196882	ERX4504060	ERS5050803	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93854	0.93903	0.09256	0.09314	0.74014	0.74059	0.47935	0.47779	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9986	9986	ERR4568386	ERX4504059	ERS5050802	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Proximal Rep2	SAMEA7292232	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292232\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Proximal Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Proximal Rep2\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Proximal Rep2 p	EuTH Proximal Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EP2_CRRA200004849-1a_HV532DSXX_L4_1.fq.gz EP2_CRRA200004849-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7168033200.0	23893444.0	E MTAB 9528:EP2 CRRA200004849 1a HV532DSXX L4	0:150 1:150	A:1903193161;C:1689671926;G:1689805787;T:1885183061;N:179265	150	150	1903193161	1689671926	1689805787	1885183061	179265	ERX4504059	ERS5050802	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93988	0.93957	0.08429	0.08448	0.74399	0.74375	0.4672	0.47077	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9987	9987	ERR4568385	ERX4504058	ERS5050801	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Proximal Rep1	SAMEA7292231	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292231\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Proximal Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Proximal Rep1\|sampling site:proximal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Proximal Rep1 p	EuTH Proximal Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:proximal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EP1_CRRA200004848-1a_HV532DSXX_L4_1.fq.gz EP1_CRRA200004848-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7993254600.0	26644182.0	E MTAB 9528:EP1 CRRA200004848 1a HV532DSXX L4	0:150 1:150	A:2055964917;C:1952736981;G:1951688671;T:2032664860;N:199171	150	150	2055964917	1952736981	1951688671	2032664860	199171	ERX4504058	ERS5050801	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.94523	0.94513	0.09369	0.09348	0.74511	0.74525	0.48633	0.48842	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9988	9988	ERR4568384	ERX4504057	ERS5050800	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Middle Rep3	SAMEA7292230	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292230\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Middle Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Middle Rep3\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Middle Rep3 p	HypoTH Middle Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HM3_CRRA200004862-1a_HV532DSXX_L4_1.fq.gz HM3_CRRA200004862-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7418093400.0	24726978.0	E MTAB 9528:HM3 CRRA200004862 1a HV532DSXX L4	0:150 1:150	A:1979368375;C:1736175227;G:1747418895;T:1954949103;N:181800	150	150	1979368375	1736175227	1747418895	1954949103	181800	ERX4504057	ERS5050800	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93389	0.93398	0.0839	0.08406	0.72147	0.72115	0.47407	0.47898	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9989	9989	ERR4568383	ERX4504056	ERS5050799	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Middle Rep2	SAMEA7292229	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292229\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Middle Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Middle Rep2\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Middle Rep2 p	HypoTH Middle Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HM2_CRRA200004861-1a_HV532DSXX_L4_1.fq.gz HM2_CRRA200004861-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7047855300.0	23492851.0	E MTAB 9528:HM2 CRRA200004861 1a HV532DSXX L4	0:150 1:150	A:1909885369;C:1626900113;G:1623501695;T:1887391464;N:176659	150	150	1909885369	1626900113	1623501695	1887391464	176659	ERX4504056	ERS5050799	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93212	0.93173	0.08713	0.08625	0.7136	0.71411	0.47182	0.46635	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9990	9990	ERR4568382	ERX4504055	ERS5050798	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Middle Rep1	SAMEA7292228	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292228\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Middle Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Middle Rep1\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Middle Rep1 p	HypoTH Middle Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HM1_CRRA200004860-1a_HV532DSXX_L4_1.fq.gz HM1_CRRA200004860-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7368139500.0	24560465.0	E MTAB 9528:HM1 CRRA200004860 1a HV532DSXX L4	0:150 1:150	A:1979116696;C:1681144383;G:1748755925;T:1958940264;N:182232	150	150	1979116696	1681144383	1748755925	1958940264	182232	ERX4504055	ERS5050798	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.90037	0.90035	0.07933	0.07951	0.72547	0.72512	0.46313	0.45076	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9991	9991	ERR4568381	ERX4504054	ERS5050797	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Middle Rep3	SAMEA7292227	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292227\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Middle Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Middle Rep3\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Middle Rep3 p	EuTH Middle Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EM3_CRRA200004853-1a_HV532DSXX_L4_1.fq.gz EM3_CRRA200004853-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	8203926600.0	27346422.0	E MTAB 9528:EM3 CRRA200004853 1a HV532DSXX L4	0:150 1:150	A:2145970242;C:1969430575;G:1966154582;T:2122170071;N:201130	150	150	2145970242	1969430575	1966154582	2122170071	201130	ERX4504054	ERS5050797	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.9358	0.93551	0.11154	0.11215	0.73908	0.73813	0.50711	0.50991	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9992	9992	ERR4568380	ERX4504053	ERS5050796	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Middle Rep2	SAMEA7292226	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292226\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Middle Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Middle Rep2\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Middle Rep2 p	EuTH Middle Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EM2_CRRA200004852-1a_HV532DSXX_L4_1.fq.gz EM2_CRRA200004852-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	8189085300.0	27296951.0	E MTAB 9528:EM2 CRRA200004852 1a HV532DSXX L4	0:150 1:150	A:2190135788;C:1917852780;G:1910200259;T:2170694756;N:201717	150	150	2190135788	1917852780	1910200259	2170694756	201717	ERX4504053	ERS5050796	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93471	0.93387	0.0982	0.0981	0.73357	0.73401	0.47523	0.47764	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9993	9993	ERR4568379	ERX4504052	ERS5050795	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Middle Rep1	SAMEA7292225	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292225\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Middle Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Middle Rep1\|sampling site:middle portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Middle Rep1 p	EuTH Middle Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:middle portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	EM1_CRRA200004851-1a_HV532DSXX_L4_1.fq.gz EM1_CRRA200004851-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7099416900.0	23664723.0	E MTAB 9528:EM1 CRRA200004851 1a HV532DSXX L4	0:150 1:150	A:1906046714;C:1656677333;G:1651795527;T:1884722014;N:175312	150	150	1906046714	1656677333	1651795527	1884722014	175312	ERX4504052	ERS5050795	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93383	0.93423	0.08879	0.08881	0.73699	0.73669	0.47814	0.47895	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9994	9994	ERR4568378	ERX4504051	ERS5050794	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Distal Rep3	SAMEA7292224	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292224\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Distal Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Distal Rep3\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Distal Rep3 p	HypoTH Distal Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HD3_CRRA200004865-1a_HV532DSXX_L4_1.fq.gz HD3_CRRA200004865-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	8040672900.0	26802243.0	E MTAB 9528:HD3 CRRA200004865 1a HV532DSXX L4	0:150 1:150	A:2167099154;C:1865357004;G:1864002622;T:2144021108;N:193012	150	150	2167099154	1865357004	1864002622	2144021108	193012	ERX4504051	ERS5050794	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.92854	0.92899	0.09996	0.09934	0.71902	0.71881	0.4815	0.47867	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9995	9995	ERR4568377	ERX4504050	ERS5050793	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Distal Rep2	SAMEA7292223	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292223\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Distal Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Distal Rep2\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Distal Rep2 p	HypoTH Distal Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HD2_CRRA200004864-1a_HV532DSXX_L4_1.fq.gz HD2_CRRA200004864-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	8313797700.0	27712659.0	E MTAB 9528:HD2 CRRA200004864 1a HV532DSXX L4	0:150 1:150	A:2273004120;C:1900982980;G:1898877384;T:2240725057;N:208159	150	150	2273004120	1900982980	1898877384	2240725057	208159	ERX4504050	ERS5050793	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.92628	0.92613	0.09471	0.09395	0.72003	0.72054	0.47995	0.47659	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9996	9996	ERR4568376	ERX4504049	ERS5050792	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	HypoTH Distal Rep1	SAMEA7292222	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292222\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:HypoTH Distal Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:hypothyroid fish\|sample name:E MTAB 9528:HypoTH Distal Rep1\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:HypoTH Distal Rep1 p	HypoTH Distal Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:hypothyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	HD1_CRRA200004863-1a_HV532DSXX_L4_1.fq.gz HD1_CRRA200004863-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7169598300.0	23898661.0	E MTAB 9528:HD1 CRRA200004863 1a HV532DSXX L4	0:150 1:150	A:1941925699;C:1655391745;G:1656382398;T:1915720427;N:178031	150	150	1941925699	1655391745	1656382398	1915720427	178031	ERX4504049	ERS5050792	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.92656	0.92587	0.09244	0.09155	0.72537	0.72577	0.483	0.48459	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9997	9997	ERR4568375	ERX4504048	ERS5050791	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Distal Rep3	SAMEA7292221	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292221\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Distal Rep3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Distal Rep3\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Distal Rep3 p	EuTH Distal Rep3 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	ED3_CRRA200004856-1a_HV532DSXX_L4_1.fq.gz ED3_CRRA200004856-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	8216298900.0	27387663.0	E MTAB 9528:ED3 CRRA200004856 1a HV532DSXX L4	0:150 1:150	A:2202070307;C:1915188230;G:1918164478;T:2180672072;N:203813	150	150	2202070307	1915188230	1918164478	2180672072	203813	ERX4504048	ERS5050791	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93043	0.92995	0.07828	0.07796	0.73799	0.73912	0.46784	0.47067	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9998	9998	ERR4568374	ERX4504047	ERS5050790	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Distal Rep2	SAMEA7292220	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292220\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Distal Rep2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Distal Rep2\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Distal Rep2 p	EuTH Distal Rep2 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	ED2_CRRA200004855-1a_HV532DSXX_L4_1.fq.gz ED2_CRRA200004855-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	6629601000.0	22098670.0	E MTAB 9528:ED2 CRRA200004855 1a HV532DSXX L4	0:150 1:150	A:1741036830;C:1583210201;G:1581636803;T:1723551874;N:165292	150	150	1741036830	1583210201	1581636803	1723551874	165292	ERX4504047	ERS5050790	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.93472	0.93506	0.0948	0.09463	0.75235	0.75235	0.49522	0.49267	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
9999	9999	ERR4568373	ERX4504046	ERS5050789	ERP123840	PRJEB40227	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E-MTAB-9528	Other	The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control.	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12		Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	EuTH Distal Rep1	SAMEA7292219	BOSTON COLLEGE	ENA FIRST PUBLIC:2021 04 11T00:31:24Z\|ENA LAST UPDATE:2020 09 04T16:33:06Z\|External Id:SAMEA7292219\|INSDC center name:BOSTON COLLEGE\|INSDC first public:2021 04 11T00:31:24Z\|INSDC last update:2020 09 04T16:33:06Z\|INSDC status:public\|Submitter Id:E MTAB 9528:EuTH Distal Rep1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:caudal fin\|phenotype:euthyroid fish\|sample name:E MTAB 9528:EuTH Distal Rep1\|sampling site:distal portion\|scientific name:Danio rerio\|strain:Tgtg:nVenus 2a nfnB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	E MTAB 9528:EuTH Distal Rep1 p	EuTH Distal Rep1 p	RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit	Experimental Factor: phenotype:euthyroid fish\|Experimental Factor: sampling site:distal portion	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP123840	Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH	ENA FIRST PUBLIC:2022 04 12\|ENA LAST UPDATE:2022 04 12	ED1_CRRA200004854-1a_HV532DSXX_L4_1.fq.gz ED1_CRRA200004854-1a_HV532DSXX_L4_2.fq.gz	fastq fastq	7261648200.0	24205494.0	E MTAB 9528:ED1 CRRA200004854 1a HV532DSXX L4	0:150 1:150	A:1943655774;C:1694798398;G:1699834504;T:1923179081;N:180443	150	150	1943655774	1694798398	1699834504	1923179081	180443	ERX4504046	ERS5050789	ERA2831606	Boston College\|European Nucleotide Archive	Boston College\|European Nucleotide Archive	2	0.92967	0.92953	0.08728	0.08781	0.73819	0.73797	0.49368	0.49233	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	nebnext	bulk	unknown	unknown	United States	2020-09-04	Adult	Adult	Multi-tissue	Multi-system
10056	10056	ERR4691987	ERX4613068	ERS5216074	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457891	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457891\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 2\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 2\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_2.fastq.gz	fastq	1291626898.0	35072619.0	ena RUN UCLA 16 10 2020 22:30:43:819 4	0:36.83 1:0	A:364596432;C:305716590;G:295397140;T:324498501;N:1418235	36	0	364596432	305716590	295397140	324498501	1418235	ERX4613068	ERS5216074	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.93311		0.08182		0.75852		0.54813		37		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10057	10057	ERR4691986	ERX4613067	ERS5216073	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457890	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457890\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 1\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 1\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_1.fastq.gz	fastq	1236033124.0	33559740.0	ena RUN UCLA 16 10 2020 22:30:43:819 3	0:36.83 1:0	A:348518065;C:293502111;G:279181983;T:313506799;N:1324166	36	0	348518065	293502111	279181983	313506799	1324166	ERX4613067	ERS5216073	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92798		0.07907		0.7697		0.5488		37		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10058	10058	ERR4691985	ERX4613066	ERS5216072	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457889	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457889\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 2\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 2\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_2.fastq.gz	fastq	1180831209.0	32069533.0	ena RUN UCLA 16 10 2020 22:30:43:819 2	0:36.82 1:0	A:328604642;C:281065336;G:278743466;T:291039015;N:1378750	36	0	328604642	281065336	278743466	291039015	1378750	ERX4613066	ERS5216072	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92319		0.08946		0.75706		0.49996		37		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10059	10059	ERR4691984	ERX4613065	ERS5216071	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457888	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457888\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 1\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 1\|scientific name:Danio rerio\|tissue type:heart	Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000		ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_1.fastq.gz	fastq	1428414407.0	38793098.0	ena RUN UCLA 16 10 2020 22:30:43:819 1	0:36.82 1:0	A:398925739;C:338731211;G:333527196;T:355553981;N:1676280	36	0	398925739	338731211	333527196	355553981	1676280	ERX4613065	ERS5216071	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92407		0.08758		0.75726		0.4969		37		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
32162	32162	SRR29095835	SRX24619914	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 4	OF 4	OF 4	6 month zebrafish with proteinuria kidney 4			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			OF_4_1.fq OF_4_2.fq	fastq fastq	4377669000.0	14592230.0	OF 4 1.fq	0:150 1:150	A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987	150	150	1194166573	999239529	1001594280	1182651631	16987	SRX24619914	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32163	32163	SRR29095836	SRX24619913	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 3	OF 3	OF 3	6 month zebrafish with proteinuria kidney 3			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			OF_3_1.fq OF_3_2.fq	fastq fastq	4798165200.0	15993884.0	OF 3 1.fq	0:150 1:150	A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459	150	150	1290466714	1114007506	1115137813	1278535708	17459	SRX24619913	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32164	32164	SRR29095837	SRX24619912	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 2	OF 2	OF 2	6 month zebrafish with proteinuria kidney 2			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			OF_2_1.fq OF_2_2.fq	fastq fastq	5661202800.0	18870676.0	OF 2 1.fq	0:150 1:150	A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813	150	150	1549085619	1287400217	1288853902	1535841249	21813	SRX24619912	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32165	32165	SRR29095838	SRX24619911	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 1	OF 1	OF 1	6 month zebrafish with proteinuria kidney 1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			OF_1_1.fq OF_1_2.fq	fastq fastq	5957895600.0	19859652.0	OF 1 1.fq	0:150 1:150	A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811	150	150	1627320757	1359602784	1360982917	1609967331	21811	SRX24619911	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32166	32166	SRR29095839	SRX24619910	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 4	NF 6	NF 6	6 month zebrafish kidney 4			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			NF_6_1.fq NF_6_2.fq	fastq fastq	5469504900.0	18231683.0	NF 6 1.fq	0:150 1:150	A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951	150	150	1480833386	1260945093	1261275041	1466430429	20951	SRX24619910	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32167	32167	SRR29095840	SRX24619909	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 3	NF 5	NF 5	6 month zebrafish kidney 3			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			NF_5_1.fq NF_5_2.fq	fastq fastq	6386781900.0	21289273.0	NF 5 1.fq	0:150 1:150	A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191	150	150	1743273279	1458330156	1460747658	1724406616	24191	SRX24619909	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32168	32168	SRR29095841	SRX24619908	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 2	NF 2	NF 2	6 month zebrafish kidney 2			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			NF_2_1.fq NF_2_2.fq	fastq fastq	5747851800.0	19159506.0	NF 2 1.fq	0:150 1:150	A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143	150	150	1564796254	1316015979	1317516650	1549501774	21143	SRX24619908	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32169	32169	SRR29095842	SRX24619907	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.				6 month zebrafish kidney 1	DN zebrafish		strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 1	NF 1	NF 1	6 month zebrafish kidney 1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP508906			NF_1_1.fq NF_1_2.fq	fastq fastq	5369089800.0	17896966.0	NF 1 1.fq	0:150 1:150	A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651	150	150	1413369042	1273865602	1277141372	1404694133	19651	SRX24619907	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
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
36586	36586	SRR1562528	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					3901027000.0	41246200.0	zebrafish data1	0:50 1:50	A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159	50	50	1065764997	896043530	867105444	1071973870	139159	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95204	0.94561	0.11416	0.11357	0.68235	0.68387	0.47537	0.47688	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36587	36587	SRR1562529	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					3298508150.0	34528793.0	zebrafish data2	0:50 1:50	A:870578872;C:780299206;G:764413584;T:883098619;N:117869	50	50	870578872	780299206	764413584	883098619	117869	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.96195	0.9525	0.05344	0.0528	0.77285	0.7737	0.44453	0.43789	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36588	36588	SRR1562530	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					5033866800.0	52047991.0	zebrafish data6	0:50 1:50	A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438	50	50	1318991279	1193979085	1179037925	1341674073	184438	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.97568	0.97028	0.03448	0.03488	0.88767	0.88785	0.17745	0.18337	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36589	36589	SRR1562531	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					4394828000.0	45714707.0	zebrafish data3	0:50 1:50	A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894	50	50	1146792341	1067826128	1033443384	1146608253	157894	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.96496	0.95999	0.03952	0.03946	0.78571	0.78518	0.51359	0.49202	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36590	36590	SRR1562532	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					3637203400.0	38182310.0	zebrafish data4	0:50 1:50	A:956604323;C:863740756;G:843429871;T:973297634;N:130816	50	50	956604323	863740756	843429871	973297634	130816	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95377	0.94653	0.0656	0.06507	0.72448	0.72541	0.4157	0.41707	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36591	36591	SRR1562533	SRX204106	SRS373224	SRP017135	PRJNA179237	Danio rerio strain:SAT Transcriptome or Gene expression	PRJNA179237	Other	Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.			Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas	Zebrafish trancriptome for protegenomic analysis	zebrafish IOB JHU transcriptome			Zebrafish transcriptome profiling for proteogenomic analysis	JHU IOB zebrafish RNA Seq	1	SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiScanSQ	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP017135					4185424200.0	44832788.0	zebrafish data5	0:50 1:50	A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807	50	50	1143949920	959926497	921201865	1160194111	151807	SRX204106	SRS373224	SRA060234	Johns Hopkins University\|Pandey Lab	Johns Hopkins University	2	0.95163	0.94301	0.12015	0.11974	0.64396	0.64514	0.49698	0.49883	50	50	B	B	biological fallback assumption	illumina	early_illumina	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-07-22	Undetermined	Undetermined	Multi-tissue	Multi-system
36761	36761	SRR10295266	SRX7008094	SRS431105	SRP023492	PRJNA206070	Nanog SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition	GSE47558	Other	Upon fertilization maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT a universal step in animal development unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish ZGA is required for gastrulation and clearance of maternal mRNAs which is achieved in part by the conserved microRNA miR 430. However the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation and a failure to activate >75% of zygotic genes. Furthermore we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre and post MZT; ribosome profiling pre MZT		pubmed:24056933		WT 2hpf Total mRNA	GSM1152440		source name:WT 2hpf Total mRNA\|tissue:Whole embryos\|strain:TUAB\|Stage:2hpf\|treatment:n1\|rna subtype:total RNA	WT 64c R0	AGR000324	AGR000324	RNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP023492			AGR000324_R1.fastq.gz	fastq	781504124.0	10282949.0	AGR000324 R1.fastq.gz	0:76	A:151879560;C:240178928;G:220957551;T:168456166;N:31919	76		151879560	240178928	220957551	168456166	31919	SRX7008094	SRS431105	SRA980383	Yale_Giraldez\|Genetics	Giraldez Lab, Genetics, Yale University	1	0.88875		0.14141		0.796		0.72154		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2019-10-16	Cleavage	Embryo	Whole Organism	All anatomical structures
37921	37921	SRR1554495	SRX685396	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_3.fq.gz	fastq	1225610154.0	12134754.0	Ovary2 Run3	0:101	A:347141358;C:303255805;G:280185540;T:294456010;N:571441	101		347141358	303255805	280185540	294456010	571441	SRX685396	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05		1e-05		1.0				101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37922	37922	SRR1554492	SRX685395	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_3.fq.gz	fastq	1192024422.0	11802222.0	Testis2 Run3	0:101	A:373380865;C:276125943;G:251033102;T:290931637;N:552875	101		373380865	276125943	251033102	290931637	552875	SRX685395	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05		1e-05		0.99997		0.0		101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37923	37923	SRR1554489	SRX685394	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_3.fq.gz	fastq	1302765670.0	12898670.0	Heart2 Run3	0:101	A:397689061;C:312745449;G:268626802;T:323141419;N:562939	101		397689061	312745449	268626802	323141419	562939	SRX685394	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05		2e-05		0.99997		1.0		101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37924	37924	SRR1554486	SRX685392	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_3.fq.gz	fastq	1211892536.0	11998936.0	Brain2 Run3	0:101	A:374228993;C:286134640;G:253944548;T:297038575;N:545780	101		374228993	286134640	253944548	297038575	545780	SRX685392	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0		0.0		1.0				101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37925	37925	SRR1554483	SRX685391	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_3.fq.gz	fastq	347516154.0	3440754.0	Ovary1 Run3	0:101	A:107805981;C:80183725;G:73617313;T:85763181;N:145954	101		107805981	80183725	73617313	85763181	145954	SRX685391	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05		4e-05		1.0				101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37926	37926	SRR1554480	SRX685390	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_3.fq.gz	fastq	1184228636.0	11725036.0	Testis1 Run3	0:101	A:340636900;C:278505979;G:259975802;T:304564724;N:545231	101		340636900	278505979	259975802	304564724	545231	SRX685390	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	1e-05		0.0		1.0				101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37927	37927	SRR1554477	SRX685389	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_3.fq.gz	fastq	1561371524.0	15459124.0	Heart1 Run3	0:101	A:454757966;C:391143691;G:334715236;T:380114024;N:640607	101		454757966	391143691	334715236	380114024	640607	SRX685389	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05		2e-05		0.99997		1.0		101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37928	37928	SRR1554474	SRX685388	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 2	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_3.fq.gz	fastq	1192445794.0	11806394.0	Brain1 Run3	0:101	A:369786121;C:268557682;G:265557417;T:288006805;N:537769	101		369786121	268557682	265557417	288006805	537769	SRX685388	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05		1e-05		1.0				101		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37929	37929	SRR1554493	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_1.fq.gz	fastq	476104278.0	9335378.0	Ovary2 Run1	0:51	A:111060704;C:120863975;G:129849761;T:114224677;N:105161	51		111060704	120863975	129849761	114224677	105161	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00027		8e-05		0.99945		0.8125		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37930	37930	SRR1554494	SRX683354	SRS686645	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF4Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary2	ZF4Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF4_Ovary_2.fq.gz	fastq	561956352.0	11018752.0	Ovary2 Run2	0:51	A:129925815;C:148479658;G:148478706;T:132824290;N:2247883	51		129925815	148479658	148478706	132824290	2247883	SRX683354	SRS686645	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022		0.0001		0.99967		0.6875		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37931	37931	SRR1554490	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_1.fq.gz	fastq	586152231.0	11493181.0	Testis2 Run1	0:51	A:145360493;C:148943988;G:151402108;T:140286245;N:159397	51		145360493	148943988	151402108	140286245	159397	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05		2e-05		0.99985		0.57142		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37932	37932	SRR1554491	SRX683353	SRS686644	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis2	ZF2Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Testis_2.fq.gz	fastq	697016337.0	13666987.0	Testis2 Run2	0:51	A:172082858;C:184634425;G:173370430;T:163527914;N:3400710	51		172082858	184634425	173370430	163527914	3400710	SRX683353	SRS686644	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	8e-05		2e-05		0.99985		0.57142		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37933	37933	SRR1554487	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_1.fq.gz	fastq	767836212.0	15055612.0	Heart2 Run1	0:51	A:192620363;C:202013249;G:191038597;T:181862075;N:301928	51		192620363	202013249	191038597	181862075	301928	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	5e-05		3e-05		0.99995		1.0		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37934	37934	SRR1554488	SRX683351	SRS686642	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Heart2	ZF2Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Heart_2.fq.gz	fastq	979886205.0	19213455.0	Heart2 Run2	0:51	A:246169086;C:264387065;G:236377487;T:227289693;N:5662874	51		246169086	264387065	236377487	227289693	5662874	SRX683351	SRS686642	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	2e-05		0.0		1.0				51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37935	37935	SRR1554484	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_1.fq.gz	fastq	654412671.0	12831621.0	Brain2 Run1	0:51	A:160544180;C:166355290;G:168608762;T:158684308;N:220131	51		160544180	166355290	168608762	158684308	220131	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	3e-05		0.0		0.99993		1.0		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37936	37936	SRR1554485	SRX683268	SRS686641	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF2Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain2	ZF2Brain1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF2_Brain_2.fq.gz	fastq	856322793.0	16790643.0	Brain2 Run2	0:51	A:210706815;C:226772546;G:212404752;T:201722093;N:4716587	51		210706815	226772546	212404752	201722093	4716587	SRX683268	SRS686641	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0		0.0		1.0				51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37937	37937	SRR1554481	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_1.fq.gz	fastq	116086965.0	2276215.0	Ovary1 Run1	0:51	A:29237121;C:30235277;G:29264328;T:27320814;N:29425	51		29237121	30235277	29264328	27320814	29425	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00022		9e-05		0.99967		0.65		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37938	37938	SRR1554482	SRX683080	SRS686559	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF3Ovary1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406\|sex:female\|tissue:Ovary\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Ovary1	ZF3Ovary1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF3_Ovary_2.fq.gz	fastq	138905844.0	2723644.0	Ovary1 Run2	0:51	A:34695180;C:38015933;G:33434207;T:32057083;N:703441	51		34695180	38015933	33434207	32057083	703441	SRX683080	SRS686559	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00016		5e-05		0.99977		0.42857		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37939	37939	SRR1554478	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_1.fq.gz	fastq	655515750.0	12853250.0	Testis1 Run1	0:51	A:152422885;C:163771947;G:179144090;T:159997538;N:179290	51		152422885	163771947	179144090	159997538	179290	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0011		0.00053		0.99829		0.67777		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37940	37940	SRR1554479	SRX683062	SRS686542	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Testis1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405\|sex:male\|tissue:Testis\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Testis1	ZF1Testis1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Testis_2.fq.gz	fastq	777594399.0	15246949.0	Testis1 Run2	0:51	A:180116528;C:202508153;G:204833105;T:186435696;N:3700917	51		180116528	202508153	204833105	186435696	3700917	SRX683062	SRS686542	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.00073		0.00032		0.99898		0.62745		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Gonad	Reproductive System
37941	37941	SRR1554475	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_1.fq.gz	fastq	810162642.0	15885542.0	Heart1 Run1	0:51	A:199665102;C:213941735;G:204361738;T:191870055;N:324012	51		199665102	213941735	204361738	191870055	324012	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	6e-05		1e-05		0.99989		0.8		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37942	37942	SRR1554476	SRX482035	SRS566618	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Heart1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404\|sex:male\|tissue:Heart\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish individual 1 heart	ZF1Heart1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Heart_2.fq.gz	fastq	1013563698.0	19873798.0	Heart1 Run2	0:51	A:249913434;C:275453651;G:247166233;T:235034199;N:5996181	51		249913434	275453651	247166233	235034199	5996181	SRX482035	SRS566618	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	4e-05		2e-05		0.99997		0.0		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Heart	Cardiovascular System
37943	37943	SRR1554472	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_1.fq.gz	fastq	679860294.0	13330594.0	Brain1 Run1	0:51	A:167202435;C:176450132;G:174468721;T:161497185;N:241821	51		167202435	176450132	174468721	161497185	241821	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0		0.0		1.0				51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
37944	37944	SRR1554473	SRX481992	SRS566490	SRP039502	PRJNA240316	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA240316	Transcriptome Analysis	Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.		pubmed:24835514			ZF1Brain1		strain:AB\|age:Reproductive Adult\|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403\|sex:male\|tissue:Brain\|birth location:University of Oregon Fish Facility\|collected by:Thomas Desvignes\|collection date:2013 10 07\|BioSampleModel:Model organism or animal	Zebrafish Brain1	ZFBrain1 1	1	Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.			miRNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP039502			ZF1_Brain_2.fq.gz	fastq	838372782.0	16438682.0	Brain1 Run2	0:51	A:206906228;C:221202670;G:210716690;T:195319694;N:4227500	51		206906228	221202670	210716690	195319694	4227500	SRX481992	SRS566490	SRA142461	University of Oregon\|JHP-Lab	University of Oregon	1	0.0		0.0		1.0				51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2014-08-22	Adult	Adult	Brain	Nervous System
39636	39636	SRR1972985	SRX993117	SRS907736	SRP057116	PRJNA280983	Danio rerio strain:CG2 Transcriptome or Gene expression	PRJNA280983	Other	CG2 homozygous diploid zebrafish line.				Model organism or animal sample from Danio rerio CG2	CG2 immune related tissues		strain:CG2\|dev stage:adult\|sex:not determined\|tissue:kidney intestine gills and spleen\|BioSampleModel:Model organism or animal	CG2 RNA seq pooled kidney intestine gills and spleen	CG2 not normalized	1	A single adult CG2 zebrafish was euthanized and the kidney intestine gills and spleen were dissected and combined for RNA extraction Trizol Life Technologies. RNA was prepared for sequencing with the TruSeq RNA kit Illumina and sequenced 2 x 100 bp paired end reads on a single lane of a HiSeq2000 Illumina. Average insert size of 280 bps.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP057116			130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_2.fq.gz 130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_1.fq.gz	fastq fastq	43788950600.0	218944753.0	CG2 non normalized	0:100 1:100	A:11515770713;C:10371712470;G:10317757450;T:11519383282;N:64326685	100	100	11515770713	10371712470	10317757450	11519383282	64326685	SRX993117	SRS907736	SRA258497	North Carolina State University	North Carolina State University	2	0.94368	0.94427	0.05435	0.05507	0.73612	0.7376	0.53132	0.53023	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	trueseq	bulk	unknown	unknown	United States	2015-08-05	Adult	Adult	Multi-tissue	Multi-system
39687	39687	SRR2051113	SRX1048368	SRS952733	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P39		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 4	P39	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4090297192.0	40497992.0	P39	0:101	A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421	101		1016157993	993771683	965986507	1113686588	694421	SRX1048368	SRS952733	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9417		0.14428		0.68937		0.5438		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39688	39688	SRR2051110	SRX1048367	SRS952731	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P37		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 3	P37	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4647442886.0	46014286.0	P37	0:101	A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479	101		1149955739	1129088798	1093234722	1274375148	788479	SRX1048367	SRS952731	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94585		0.12571		0.68633		0.52597		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39689	39689	SRR2051112	SRX1048366	SRS952732	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P36		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 2	P36	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4296894611.0	42543511.0	P36	0:101	A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407	101		1050039699	1061123166	1022913715	1162094624	723407	SRX1048366	SRS952732	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94977		0.13188		0.70976		0.52728		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39690	39690	SRR2051109	SRX1048365	SRS952730	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P35		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Severe phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 3.0 uM CPO Rep 1	P35	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4094752706.0	40542106.0	P35	0:101	A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167	101		1009779802	1004374749	969241794	1110655194	701167	SRX1048365	SRS952730	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94442		0.13203		0.70023		0.53953		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39691	39691	SRR2051102	SRX1048364	SRS952729	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P29		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 4	P29	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4983571896.0	49342296.0	P29	0:101	A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841	101		1247122516	1202173111	1173654831	1359775597	845841	SRX1048364	SRS952729	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94329		0.13234		0.68286		0.51586		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39692	39692	SRR2051100	SRX1048363	SRS952727	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P28		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 3	P28	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4032678914.0	39927514.0	P28	0:101	A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488	101		1015356577	970369004	937306142	1108957703	689488	SRX1048363	SRS952727	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.93887		0.13869		0.69079		0.52237		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39693	39693	SRR2051101	SRX1048362	SRS952728	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P26		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 2	P26	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz	fastq fastq fastq fastq	6526758875.0	64621375.0	P26	0:101	A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228	101		1635664768	1568967965	1518148006	1802863908	1114228	SRX1048362	SRS952728	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.93822		0.15203		0.68609		0.53171		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39694	39694	SRR2051096	SRX1048361	SRS952726	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P25		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Moderate phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 1.0 uM CPO Rep 1	P25	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4185957322.0	41445122.0	P25	0:101	A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428	101		1081936223	978799105	956795307	1167714259	712428	SRX1048361	SRS952726	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9288		0.17032		0.6801		0.51298		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39695	39695	SRR2051095	SRX1048360	SRS952725	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P19		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 4	P19	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4293546461.0	42510361.0	P19	0:101	A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822	101		1062707728	1045602693	1011860446	1172670772	704822	SRX1048360	SRS952725	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94381		0.13697		0.69051		0.51415		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39696	39696	SRR2051094	SRX1048359	SRS952724	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P18		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 3	P18	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4257944163.0	42157863.0	P18	0:101	A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125	101		1044532409	1049992329	1010166097	1152524203	729125	SRX1048359	SRS952724	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94262		0.14592		0.69014		0.52498		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39697	39697	SRR2051093	SRX1048358	SRS952723	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P17		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 2	P17	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4278385553.0	42360253.0	P17	0:101	A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139	101		1040955882	1060023973	1019487833	1157186726	731139	SRX1048358	SRS952723	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94697		0.14458		0.69643		0.53451		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39698	39698	SRR2051092	SRX1048357	SRS952722	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					P15		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:mild phenotype\|BioSampleModel:Model organism or animal	D. rerio OP 0.1 uM CPO Rep 1	P15	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4341747499.0	42987599.0	P15	0:101	A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377	101		1052621077	1088380866	1041958433	1158051746	735377	SRX1048357	SRS952722	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94563		0.153		0.69822		0.54133		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2015-06-04	Larval	Larval	Whole Organism	All anatomical structures
39699	39699	SRR2051091	SRX1048356	SRS952721	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN9		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 4	CN9	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4220387212.0	41786012.0	CN9	0:101	A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235	101		1031722430	1044497851	1005706674	1137783022	677235	SRX1048356	SRS952721	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.95231		0.14084		0.69682		0.52966		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39700	39700	SRR2051090	SRX1048354	SRS952719	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN8		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 3	CN8	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz	fastq fastq fastq fastq	5835502553.0	57777253.0	CN8	0:101	A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739	101		1424369529	1441755207	1391851806	1576540272	985739	SRX1048354	SRS952719	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94643		0.12925		0.70725		0.52949		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39701	39701	SRR2050894	SRX1048353	SRS952718	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN7		breed:Wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 2	CN7	1	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz	fastq fastq fastq fastq	4789094477.0	47416777.0	CN7	0:101	A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016	101		1160528098	1197558725	1155573375	1274638263	796016	SRX1048353	SRS952718	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.9501		0.14828		0.69966		0.52764		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
39702	39702	SRR2050892	SRX1048352	SRS952717	SRP059060	PRJNA285816	Danio rerio Raw sequence reads	PRJNA285816	Whole Genome Sequencing	Here we have generated and validated zebrafish models for mild moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans including acetylcholinesterase inhibition NMDA receptor activation calcium dysregulation and inflammatory and immune response.					CN5		breed:wild type\|dev stage:larvae\|sex:not applicable\|tissue:whole organism\|treatment:Control\|BioSampleModel:Model organism or animal	D. rerio OP Control Rep 1	CN5	CN5 EL4506 TGACCA	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP059060			CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz	fastq fastq fastq fastq	4526144512.0	44813312.0	CN5	0:101	A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159	101		1109966549	1116619353	1075422479	1223366972	769159	SRX1048352	SRS952717	SRA271167	Mississippi State University\|IGBB	US Army ERDC	1	0.94604		0.14084		0.69004		0.53407		101		B		usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2016-03-17	Larval	Larval	Whole Organism	All anatomical structures
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
39824	39824	SRR2168748	SRX1153634	SRS1036568	SRP062468	PRJNA293022	Danio rerio heart chamber specific transcriptome	PRJNA293022	Whole Genome Sequencing	Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus					ASWT Heart chamber transcriptome		breed:ASWT\|age:2 years\|dev stage:Adult\|sex:not applicable\|tissue:Heart Chambers\|BioSampleModel:Model organism or animal	Zebrafish ASWT heart bulbus arteriosus transcriptome	Zebrafish bulbus arteriosus	Bulbus arteriosus	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<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>	SRP062468			ZFBulbouse_cat_R1.fastq.gz ZFBulbouse_cat_R2.fastq.gz	fastq fastq	31137941450.0	154148225.0	Zebrafish bulbus arteriosus	0:101 1:101	A:8841038901;C:6663109706;G:6831238323;T:8799856408;N:2698112	101	101	8841038901	6663109706	6831238323	8799856408	2698112	SRX1153634	SRS1036568	SRA289351	CSIR-IGIB	CSIR- Institute of Genomics and Integrative Biology	2	0.81876	0.77794	0.54672	0.51003	0.7162	0.72752	0.54114	0.5421	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	India	2016-03-01	Adult	Adult	Heart	Cardiovascular System
39825	39825	SRR2168740	SRX1153633	SRS1036568	SRP062468	PRJNA293022	Danio rerio heart chamber specific transcriptome	PRJNA293022	Whole Genome Sequencing	Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus					ASWT Heart chamber transcriptome		breed:ASWT\|age:2 years\|dev stage:Adult\|sex:not applicable\|tissue:Heart Chambers\|BioSampleModel:Model organism or animal	Zebrafish ASWT atrium specific transcriptome	Zebrafish Atrium	Atrium	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2500	<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>	SRP062468			ZFAtrium_GTGAAA_L006_cat_R2.fastq.gz ZFAtrium_GTGAAA_L006_cat_R1.fastq.gz	fastq fastq	28208507150.0	139646075.0	Zebrafish Atrium	0:101 1:101	A:8151737615;C:5894384726;G:6027846905;T:8129189369;N:5348535	101	101	8151737615	5894384726	6027846905	8129189369	5348535	SRX1153633	SRS1036568	SRA289351	CSIR-IGIB	CSIR- Institute of Genomics and Integrative Biology	2	0.83701	0.79433	0.58576	0.54496	0.72486	0.73766	0.55105	0.54713	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	India	2015-09-08	Adult	Adult	Heart	Cardiovascular System

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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");;